Abstract Although studies have explored how soil microbial diversity and soil multifunctionality respond to land‐use change at local scales, they have rarely been explored at larger scales and across different climatic and soil environmental conditions. By sampling 40 paired sites of land‐use change from natural forests to agricultural lands (including croplands and orchards) along the middle and lower Yangtze River, combined with a global meta‐analysis, we investigated the effects of land‐use change and climate on the alpha and beta diversity of soil bacterial and fungal functional groups (FGs) and their associated soil multifunctionality at a regional scale. Our results showed that land‐use change strongly changed the diversity of soil bacterial and fungal FGs and decreased multifunctionality, which was supported by our meta‐analysis at a global scale. Direct effects of land‐use change and climate and their interaction, together with changes in soil environmental variables, were the main determinants of the land‐use change‐induced changes in the diversity of soil bacterial or fungal FGs. The land‐use change‐induced decrease in multifunctionality was mainly associated with the direct effect of forest conversion, soil fertility and diversity of fungal FGs. Furthermore, climate also regulated the effects of land‐use change on multifunctionality by affecting soil fertility and fungal FGs diversity along the Yangtze River. Synthesis and applications. Taken together, our findings highlight the important effects of land‐use change, climate and their interactions on microbial diversity and multifunctionality and suggest that effective land‐use management and climate change mitigation strategies should be adopted to protect biodiversity and ecosystem function in the Yangtze River Basin.