Under the influence of Holocene climatic fluctuations, a dual agricultural system demarcated by the line of Qinling Mountains-Huaihe River—domination of rice (Oryza sativa) cultivation in the south, and prevalence of dryland agriculture centered on foxtail millet (Setaria italica) and common millet (Panicum miliaceum) in the north—was formed in China. The development of these systems elevated the economic and cultural levels of the Yangtze River and Yellow River basins above surrounding regions, with both the agricultural systems diffusing outwards through distinct pathways and gradually intensifying their integration. Traditionally, the middle-lower reaches of Yangtze River, as the rice domestication center, has been regarded as the core area of rice culture and a typical representative of the “southern rice-northern millet” dichotomy. However, recent archaeobotanical studies revealed the widespread distribution of northern millet crops in the southern regions, suggesting the existence of mixed rice-millet cultivation. This discovery has challenged traditional cognition, but there are still many questions and gaps in the southward transmission path of dryland crops and the formation mechanism of mixed farming. The Shixingshan site in Huangshan District, Anhui Province, located at the transitional zone between the Lower Yangtze Plain and the southern Anhui mountains, provides critical materials for addressing these questions. With cultural deposits spanning from the early Shang Dynasty (3 572-3 450 cal. BP) to the late Warring States Period (2 326-2 144 cal. BP), we used phytolith analysis and AMS ¹⁴C dating to systematically reconstruct agricultural structures, document shifts in crop harvesting practices and preliminarily explore the driving forces behind millet’s southward spread in this study. We deepened the understanding of complexity of agriculture in the lower reaches of Yangtze River. Chronological sequences were established after AMS ¹⁴C dating of floated charcoal samples (Beta Analytic Laboratory, IntCal20 calibration), in combination with artifact typology (pottery, stone tools). The research focused on profile samples from the T02 southern wall (nine layers) of Excavation Area Ⅲ and five ash pit samples. Standardized phytolith extraction protocol was applied to the selected samples:5 g soil samples underwent organic matter oxidation with hydrogen peroxide (30% H₂O₂), mineral removal with hydrochloric acid (10% HCl), followed by zinc bromide heavy liquid flotation (density 2.3-2.4). A Nikon microscope (500×) was utilized for the phytolith identification of 3 614 phytoliths counted across layers. A total of over 30 phytolith morphotypes were identified, dominated by long-saddle, short-saddle, rondel, bilobate, elongate echinate, smooth-elongate, rectangular, square and acicular types. Notably, several diagnostic crop-derived phytoliths were identified, such as the Ω-undulated type from foxtail millet husks, the double-peaked type from rice glume cells, the parallel bilobate type from rice stems, and the bulliform type from rice leaves. Among the five pit samples from the Shihingshan site, two yielded rice phytoliths. The stratigraphic samples from the Late Neolithic Age to Warring States Period contained both rice (peaking at 11.3%) and millet (peaking at 2.3%). The earliest securely dated Ω-type phytoliths of millet appeared in the early Shang layers (3 572-3 450 cal. BP), confirming that millet’s arrival was no later than the Shang Dynasty. The mixed rice-millet pattern (without broomcorn millet) resembles the findings in Hunan, Hubei and Jiangxi, suggesting cultural exchange influences. By analyzing the crop harvesting method through phytolith ratio, it was found that:in the early Shang Dynasty, the proportion of double-peak phytoliths in rice husk was significantly higher than that in stem and leaf phytoliths (the sum of dumbbell and fan-shaped phytoliths), indicating that the ears were picked and harvested; by the Warring States Period, the proportion of husk and stem and leaf phytoliths was close, reflecting the popularity of continuous stalk harvesting. This change is confirmed by the widespread use of iron sickles in the middle and late Warring States Period, highlighting the impact of agricultural technological progress on harvesting practices. The discovery of the Shixingshan site confirms “rice-dominant, millet-supplementary” agriculture in southern Anhui, which was driven by both topographic constraints (mountain-limited rice expansion) and cultural interactions (middle reaches of the Yangtze River and Jiangxi influences). The popularization of iron tools during the Warring States Period directly promoted the transformation of harvesting methods, improving resource utilization efficiency. This study provides critical evidence for understanding the formation mechanism of mixed farming in the middle-lower reaches of Yangtze River and the route of millet cultivation to the south, and also lays an important foundation for understanding the evolution of ancient harvesting practices and its productivity drivers.