Abstract: This study aimed to explore the nutritional components and their differences in different Ganoderma lucidum varieties in Zhangzhou, Fujian, in order to provide reference for the rational use of Ganoderma lucidum. By taking the fruiting bodies of Ganoderma sinense and G. lucidum (Leyss. ex Fr.) Karst under the same growth environment and site conditions as the research object, the nutritional components were determined by using the techniques such as inductively coupled plasma mass spectrometry, and spectrophotometry. The differences in the contents of total triterpenoids, total polyphenols, total flavonoids and other nutrients in different varieties of Ganoderma lucidum were compared to evaluate the nutritional quality of Ganoderma lucidum. The results showed that: in terms of basic components and nutritional components, G. lucidum (Leyss. ex Fr.) Karst GL-2 exhibited significantly higher levels of protein (22.0 g·hg⁻¹), soluble sugar (0.27%), crude polysaccharide (1.00 g·hg⁻¹), and total triterpenoids (2.92 g·hg⁻¹) compared to other varieties. Conversely, G. lucidum (Leyss. ex Fr.) Karst GL-1 demonstrated the highest content of fat (3.6 g·hg⁻¹) and crude fiber (50.6%). In terms of amino acid composition, G. lucidum (Leyss. ex Fr.) Karst GL-2 possessed the highest total amino acid content (12.25 g·hg⁻¹), with all 17 amino acids being significantly more abundant than that in the Ganoderma sinense. In terms of fatty acid composition, G. lucidum (Leyss. ex Fr.) Karst exhibited a higher proportion of saturated fatty acids, such as stearic acid and arachidonic acid. Notably, the linolenic acid content in GL-2 (0.652%) was 7.8 times greater than that in Ganoderma sinense GS-1, while Ganoderma sinense GS-1 had a higher proportion of unsaturated fatty acids, such as oleic acid (55.2%), and GS-2 had a higher proportion of linoleic acid (40.0%). In terms of mineral element content, Ganoderma sinense GS-2 contained higher levels of calcium (3000 mg·kg⁻¹), iron (1250 mg·kg⁻¹) , and zinc (46.8 mg·kg⁻¹) compared to the G. lucidum (Leyss. ex Fr.) Karst. G. lucidum (Leyss. ex Fr.) Karst GL-2 demonstrated notable advantages in the concentrations of fundamental components such as protein, soluble sugars, and crude polysaccharides, as well as total triterpenoids and amino acids, indicating its potential as the raw material with significant nutritional functionality. The levels of mineral elements, including calcium, iron, zinc, and selenium, alongside the unsaturated fatty acids such as oleic and linoleic acids, were particularly pronounced in Ganoderma sinense GS-2. Notably, the calcium, iron, and zinc contents in Ganoderma sinense GS-2 and the selenium content in Ganoderma sinense GS-1 indicated their potential application in the nutritional enrichment and targeted metabolic regulation. The specificity of different varieties significantly influenced the accumulation of functional components, such as total polyphenols and flavonoids. Specifically, Ganoderma sinense GS-2 exhibited the highest level of total polyphenol, while G. lucidum (Leyss. ex Fr.) Karst GL-1 had the highest content of total flavonoids. In summary, the comprehensive nutritional benefits of G. lucidum (Leyss. ex Fr.) Karst GL-2, along with the distinctive mineral element profile of Ganoderma sinense, could provide reference for the variety breeding and the development of functional products.