This study addressed three important aims: (1) undermining the previously obtained raw data about wood-decaying fungi (WDF) distribution and continuously investigating permanent plots to address certain scientific questions in ecology, (2) resolving the higher-level phylogeny of WDF with the help of multiple loci, and (3) testing and estimating the medicinal values of species that are closely related to well-known medicinal species. More than 1200 species and 2469 strains of WDF in China were identified from 28908 specimens collected from a series of field investigations. Using these materials, studies in multiple disciplines, such as ecology, taxonomy and phylogeny, and medicine, have been performed. With respect to ecology, the diversity of wood-decaying polypores significantly differed among a boreal forest zone, a temperate and warm temperate forest zone, and a tropical and subtropical forest zone. For instance, from north to south, the number and proportion of brown-rot species and the proportion of species found on fallen trunks were both decreased. The ecological patterns of wood-decaying polypores on gymnosperm and angiosperm trees were also explored by a case study in Northeast China. Although the total species richness was similar between the two tree groups, several other characteristics were significantly different, such as community structure and richness in certain substrates. The taxonomy and phylogeny of wide samples were referred to and their phylogenetic positions were resolved or at least partially established. In particular, phylogenetic knowledge about four genera, Fomitiporia, Ganoderma, Inonotus and Perenniporia, which include medicinal species, was essential for further research to determine the medicinal values of these types of fungi. Among these medicinal species, we mainly focused on Inonotus obliquus for its medicinal purposes. Polyphenols, polysaccharides and lanostane-type triterpenoids, extracted from the sterile conk of this species, could dramatically decrease levels of free radicals, DPPH and hydroxyl radicals, respectively. The metabolic profiles (both production and composition) of cultured I. obliquus mycelia could be altered by co-culture with other medicinal species or by induction of S-nitrosylation and denitrosylation, which may enhance the antioxidant capacity of I. obliquus.