Leaf δ¹⁵N and δ¹³C are important functional traits in biogeographic studies of forest ecosystems. However, little is known about their relationships with soil fungal biodiversity, ectomycorrhizal and plant pathogenic abundance at large scales. In this study, leaf and soil samples were collected from 33 forest reserves along a large range across China to explore the associations between leaf δ¹⁵N and δ¹³C and soil fungal biodiversity, ectomycorrhizal and plant pathogenic relative abundance, using molecular and stable isotope techniques. Leaf δ¹⁵N was significantly positively correlated with the soil fungal Shannon index, significantly negatively correlated with the relative abundance of plant pathogens, and significantly positively correlated with the relative abundance of ectomycorrhizas. Leaf δ¹³C was significantly positively correlated with the relative abundance of ectomycorrhizas and significantly inverted unimodal correlated with the relative abundance of plant pathogens. Soil–plant–microbial interactions may contribute to variations in leaf δ¹⁵N, δ¹³C, and soil fungal communities among different types of forest ecosystems. Temperature and precipitation were the main factors that affected large-scale latitudinal and longitudinal biogeographic patterns. Leaf δ¹⁵N was mainly affected by the relative abundance of ectomycorrhizal fungi and leaf δ¹³C was affected by the mean annual temperature and mean annual precipitation. Leaf δ¹⁵N and δ¹³C may be indicators that reflect soil fungal communities in forest ecosystems.