Soil ectomycorrhizal and saprotrophic fungi play pivotal roles in plant performance and ecosystem functioning. However, the effects of forest secondary succession on their abundance, diversity, and community structure remain unclear. We examined ectomycorrhizal and saprotrophic communities (Illumina Sequencing and FUNGuild database) in five forest secondary successional stages (20-, 32-, 47-, 61-, and > 200-year-old stands). Our results showed that ectomycorrhizal and saprotrophic communities varied with successional stages. The relative abundance of ectomycorrhizal fungi decreased from early to late stages but the relative abundance of saprotrophic fungi increased. In contrast to the abundance, diversity of ectomycorrhizal fungal communities increased with the succession, while saprotrophic fungal diversity dropped in the early successional stages and recovered later stages. Furthermore, there were significant differences in the community structure of ectomycorrhizal and saprotrophic fungi among different successional stages, and the main driving factor (tree productivity) of the shifts in two community structures was similar. Interestingly, there was a significant negative correlation between the variations in relative abundance and community structure of ectomycorrhizal and saprotrophic fungi along the secondary succession, which implied the interactions between ectomycorrhizal and saprotrophic fungi during the successional process. These results indicated that the secondary succession might not only increase decompositions of organic matter by increasing saprotrophic fungal abundance, but also stimulate the return of saprotrophic fungal diversity, which may be beneficial to plant function and ecosystem stability.