Understanding what controls the soil organic matter (SOM) storage and its stability is important to predict how SOM will respond to environmental changes. The role of mycorrhizal fungi in mediating soil carbon (C) and nitrogen (N) cycling is increasingly recognized. However, how mycorrhizal fungi could affect C distribution and N demand of different soil fractions is largely unknown. Here, we compiled a global dataset of C and N concentrations in different SOM fractions from arbuscular mycorrhizal (AM) and ectomycorrhizal (EcM) dominated ecosystems, covering major biomes, including tropical forest, temperate forest, boreal forest, and grassland. Based on this dataset, we evaluated the effect of mycorrhiza symbiosis on C storage and C: N stoichiometry of SOM fractions with different stability. We found that for both topsoil and subsoil, bulk soil C storage and C: N ratio in EcM ecosystems were higher than those in AM ecosystems, and a similar pattern was also observed in the particulate organic matter fraction (POM). However, the C storage in the mineral-associated organic matter fraction (MAOM) was not different between AM and EcM ecosystems. Moreover, with the increase in bulk soil C concentration, the C storage in topsoil MAOM reached a stable level in EcM ecosystems but continued to increase in AM ecosystems. With the increase in soil N concentration, bulk soil C storage of EcM ecosystems increased more rapidly than that of AM ecosystems, which was mainly driven by the increase in POM C storage. Our study highlights that soil C storage and relative stability are different between AM and EcM ecosystems. Although EcM ecosystems have a higher soil C storage and lower N demand per unit soil C, most C is distributed in relative labile POM. Therefore, SOM in EcM ecosystems could be more susceptible to disturbances caused by land use and climate changes.