Well-known as the source of an elixir in ancient China, Ganoderma lucidum (the lingzhi mushroom) also provides important clues in contemporary studies to the origins of traditional Chinese medicine. Since remains suspected to be those of Ganoderma lucidum are often discovered in archaeological sites, their identification has become a focus of much research. Traditionally, Ganoderma lucidum is identified by its appearance and the observation of spores. However, sometimes these two methods are not practical because ancient Ganoderma lucidum remains cannot be kept intact easily and the workload is quite heavy. In order to identify Ganoderma lucidum remains more efficiently, we conducted micro-CT imaging and 3D reconstruction of Ganoderma lucidum remains unearthed from Tianluoshan Site. The reconstructed images, compared with standards, showed conclusive identification of the Ganoderma lucidum body, demonstrating a new method for the identification of ancient Ganoderma lucidum remains. Differing from the traditional method of appearance contrast, 3D reconstruction is not only fast and convenient, but also not affected by the appearance of remains. Therefore, this method can also provide reference for the identification of other ancient plants with characteristic structures.