Climate warming is one of the most serious threats to soil biodiversity and ecosystem stability. Straw return has been extensively recommended as an environmentally friendly management to increase soil health and agricultural productivity. However, little is known about their interactive effects on microbial communities and soil functioning. We investigated the effects of soil warming, straw return, and their interactions on soil microbial communities, functional genes, enzyme activities related to C, N and P cycling, and multifunctionality in a two-factorial experiment in a wheat-maize rotation system. Soil warming decreased fungal diversity (by 20%) and functional genes associated with organic matter decomposition, N fixation, nitrification, denitrification, and organic P mineralization compared with ambient temperature. Soil multifunctionality mediated by enzyme activities were reduced under warming because of lower soil moisture, nutrient availability, and root-derived labile organic matter inputs. The close relationships of microbial diversity and functional genes with soil multifunctionality highlighted the importance of soil biodiversity in maintaining agroecosystem functioning related to nutrient cycling. Under soil warming and ambient temperature, straw return resulted in higher bacterial diversity (by 3.6%) and microbial functional genes abundances of C, N and P cycling compared to straw removal, and consequently raised soil multifunctionality. This was primarily because straw buffered soil temperature amplitude and moisture variation, as well as the additional nutrient supply within the added straw. Overall, straw return created favorable habitats for microorganisms, and thereby mitigated the adverse effects of warming on microbial communities and soil functionality. Our study provided the possibility to increase soil biodiversity and further ecosystem services related to organic matter decomposition and nutrient turnover by straw addition, especially under climate warming.