Organic cultural relics containing sulfur and iron compounds will be subject to biological and chemical erosion during long-term immersion in the ocean. After excavation, these compounds will become unstable in the transition from a low-oxygen marine environment to aerobic air, which may lead to reduction of the mechanical stability of organic cultural relics and their chemical deterioration. At present, most of the ancient shipwrecks salvaged in the world are made of wooden organic materials, among which the most famous are the Vasa in Stockholm, Sweden and the Mary Rose in Portsmouth, England, with their hull wood degraded due to the accumulation of reduced sulfur compounds transformed by sulfate-reducing bacteria in the sea and iron ions (Ⅱ) from corroded iron bolts on the hulls. According to research, several tons of reduced sulfides have accumulated in the hull wood of the Vasa, and about two tons of sulfur or sulfuric acid exists in a hull weighing 280 tons. China’s Huaguangjiao Ⅰ shipwreck of the Southern Song Dynasty has large amounts of ironware. In the process of ship manufacturing, a large number of iron nails were embedded to strengthen the hull. These iron objects may pose hidden dangers to the wooden hull before and after the excavation. In order to protect the Huaguangjiao Ⅰ shipwreck, a batch of samples was selected according to the actual situation to scientifically evaluate the status of the hull, so as to provide a basis for formulating the protection scheme in the next step. In this study, several samples were selected from the hull of Huaguangjiao Ⅰ to determine its moisture content; the molecular structure changes, chemical components, ion content and phase composition of wood samples were analyzed using a Fourier transform infrared spectrometer (FTIR), an ion chromatograph (IC), an element analyzer, an inductively coupled plasma optical emission spectrometer (ICP-OES) and an X-ray diffractometer (XRD) to evaluate its current situation. Through these analyses, it was found that, with an average moisture content of 447.9%, the moisture content of its pine components is generally higher than that of normal modern pine wood. Compared with the hull wood of a Song Dynasty shipwreck (300% moisture content) in Quanzhou Bay and that of Xiaobaijiao Ⅰ(210% moisture content) in Ningbo, the hull components of Huaguangjiao Ⅰ suffer more serious degradation. The extract content by 1% NaOH from Huaguangjiao Ⅰ water-saturated archaeological wood is much higher than that from modern wood, and its average content of total cellulose accounts for only 27% of that of modern wood, indicating that cellulose and hemicellulose have been seriously degraded. The lignin content is increased, and the average ash content is 68 times that of modern pine. It can be seen from the infrared spectrum that compared with modern pine wood, the chemical composition and structure of the archaeological wood of Huaguangjiao Ⅰ have been changed, the hemicellulose has been seriously lost, the cellulose molecular chain has been partially degraded, and the molecular chain crystal structure has been damaged. The concentration of sulfate ion in a wood-soaking solution of Huaguangjiao Ⅰ is high. The content of iron ion according to ICP-OES test results is very high, indicating that the inorganic compounds in wood are mainly iron. In combination with the high concentration of sulfate ion in the soaking solution, this indicates that the iron and sulfur compounds in the hull have not been removed. XRD results confirm the existence of iron and sulfur compounds—pyrite (FeS₂), goethite and sulfate in the hull. According to the literature, the Huaguangjiao Ⅰ shipwreck is a cultural relic found in a tropical area. The conservation and preservation of sulfur- and iron-containing wooden cultural relics salvaged from a warm and salty tropical sea is not only a challenge, but also a new topic. Based on scientific evaluation of the current situation of the Huaguangjiao Ⅰ shipwreck components, it is hard to be optimistic about preservation of the shipwreck, as the degree of wood decay and damage is very serious. This is the key problem that cultural relic conservators must face and solve.