Soil microbial diversity is a key control over soil element cycling and ecosystem functioning, but how the keystone species regulate the association between soil microbial diversity and ecosystem functioning (particularly, the whole-community and specialized species driving) under land use change remain unresolved. Here we identified the relationship of microbial diversity [e.g., soil phospholipid fatty acids (PLFAs) richness and composition, ammonia-oxidizing archaea and bacteria (AOA and AOB) communities] with both the broad (i.e. microbial basal respiration) and specialized function (i.e. nitrification rate) in the wood land, shrubland and adjacent cropland in subtropical China. The microbial richness was significantly positively related to the broad function, but negatively correlated with the keystone species across different land use types. The relationship of biodiversity with the broad ecosystem functioning varied with land use change, with stronger relationship in the afforested land compared to the cropland. In contrast to the broad function, land use change did not significantly affect the specialized function (i.e. nitrification rate), but the specialized function was positively related to the AOA richness in the cropland. Additionally, the specialized function was predominately driven by the keystone species composition in AOA and AOB communities and indirectly regulated by soil environmental factors (particularly, soil temperature) across land use change. Overall, our results provided direct experimental insight into the mechanisms underlying the role of the keystone species in regulating below-ground ecosystem functioning under land use change, more especially, our findings also revealed shift in the maintaining mechanisms of ecosystem function from the broad function (i.e. niche compensation effect) to the specialize function (i.e. identity effect).