In Asian countries, the sclerotia of the wild-grown fungus Pachyma hoelen (“Fuling”), have been used as food and as medicinal products for centuries. To close the knowledge gaps about the value and possible environmental impacts, the occurrence, distribution, and associations of a range of elements (Ag, Al, As, Ba, Cd, Co, Cr, Cs, Cu, Li, Mg, Mn, Ni, Pb, Rb, Sb, Sr, Tl, U, V, and Zn) were studied in the inner (core) and outer (shell) morphological parts of the sclerotia from a diverse collection in Southern China. Quality of forest and agricultural soil in terms of a geogenic element source and composition can be considered as the main factor determining the occurrence of minerals in sclerotia through the host wood, largely of Pinus yunnanensis, while the anthropogenic impact (basically at remote rural areas of cultivation) in Southern China was negligible. In general, the mean concentration of each element in the outer part was significantly higher than that in the inner part (t-test, p < 0.01), except for Ag. The concentration of a given element in the outer part tended to have a positive relationship with that in the inner part, except for Cu, Se, Ag, and Zn. The elements in different morphological parts of sclerotia present different relation patterns. Compared to the outer part, there were stronger associations of elements in the inner part, suggesting homeostatic regulation of multiple elements in the inner parts. Further study on the sclerotia, infected wood substrate, and surrounding soil from a range of wild sample collections and intentional cultivation should provide a more complex view and allow assessment of the relationship between minerals and bioactive organic compounds produced by P. hoelen.