Endophytic fungal natural products, especially sulfur- or sulfone-containing scaffolds, have attracted increasing attention as a valuable resource for drug development. Ascomycotol A (1), a polyketide with an unprecedented 4-oxa-12-thiabicyclo[7.3.1]tridecane sulfur-containing scaffold, and ascomycotols B (2) and C (3) featuring rare sulfone functional moieties, were purified from the mushroom (Ganoderma species)-associated endophytic Ascomycota sp. GLQ01 and Trichoderma harzianum GLQ03. Their chemical structures were assigned using nuclear magnetic resonance data, electronic circular dichroism calculations, and X-ray diffraction methods. A possible biosynthetic pathway of compounds 1-3 was speculated, involving two consecutive S-nucleophilic addition reactions and atypical incorporation of both l-Phe and d-Phe residues. Finally, biological activity studies revealed that compounds 1 and (+)-2 exhibit the potential of anti-inflammatory activity, and compound 1 has a dose-dependent protective effect on age-related renal fibrosis in vitro.