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Enhancing cropping intensity is the most effective and significant method to improve regional crop production and ensure food security. However, our understanding of the impacts of reduced cropping intensity on soil quality and ecosystem multifunctionality (EMF) with soil depth remains incomplete in tropical regions. Here, we performed a 4‐year field experiment to estimate the impacts of cropping intensity (continuous cropping, winter fallow, and annual fallow) on soil quality and EMF depending on soil depths. We found that reduced cropping intensity improved soil quality at the topsoil (0–10 cm), while it had no significant influences on soil carbon (C) and nitrogen (N) storage, as well as soil EMF at 0–40 cm. Soil microbes were limited by C and P but not co‐limited by N in all three cropping systems. Reduced cropping intensity exacerbated microbial C limitation at 0–10 cm due to reduced additional C resources (i.e., rice straw and manure) input. Redundancy analysis and Pearson correlation showed that soil N significantly affected the C‐, N‐, and P‐acquisition enzyme activities, and correlated positively with soil organic C, microbial biomass C, and available P. In conclusion, short‐term reduction in cropping intensity improves topsoil quality but not soil EMF under paddy‐upland rotations in the tropical region. [ABSTRACT FROM AUTHOR]