Soil salinization is a widespread environmental problem adversely impacting global food production. Increasing soil organic matter (SOM) could alleviate salt stress, but soil salinity and SOM have differing effects on microbial diversity and activities. We explored how the relationships between soil biodiversity and multifunctionality were altered by soil salinity and SOM. We collected soils from the wheat-maize cropping system in the North China Plain and categorized soils according to salinity and SOM. Soil functions related to carbon, nitrogen, phosphorus, and micronutrient processing were measured as metrics of soil multifunctionality (SMF) characterization. We found significant positive relationships between SMF and bacterial diversity but not fungal diversity in soils with high SOM (>15 mg/kg) and low EC (<4 ds/m). The diversity and abundance of sensitive bacteria were more strongly correlated with SMF than those of non-sensitive bacteria. SOM directly and indirectly impacted SMF through changes in sensitive bacterial abundance, while soil EC impacted SMF via altered sensitive bacterial diversity. With respective to individual soil function, carbon and micronutrient cycling were predominantly determined by bacterial diversity. Our findings suggest coupling decreased salinization with the increase of SOM could increase soil multifunctionality by increasing diversity and abundance of sensitive soil microbes. These findings highlight the importance of sensitive microbial taxa to sustaining soil ecosystem functioning in croplands.