AbstractStraw return is an important nature‐based solution to identify optimal management practices to maintain cropland soil health and food security. However, there is still limited information available regarding the impacts of different straw return strategies on soil health, especially when considering a comprehensive assessment of soil physical, chemical and biological characteristics. Soil microorganisms are the core and key to maintaining soil health. The present research aims to determine the impact of straw return to different depths on soil health index (SHI) and crop productivity across different soil layers. We conducted a 3–year field experiment with four treatments: a blank control with no straw return (NR), straw return treatments with shallow return (SR), mulch return (MR) and deep return (DR), and the straw application rate was 10,500 kg/ha. The results showed that it was the microbial indicators that dominated the effects on soil health, rather than soil organic carbon (SOC). Specifically, we found that the SR treatment exhibited the highest extracellular enzyme activities of both hydrolases and oxidases in the subsoil, and the peroxidase (PEO) activity was 758.99 nmol/g/h. In addition, compared with MR and DR treatments, the abundance of symbiotroph fungi in SR treatment increased by 78.41% and 54.38%, releasing more nutrients to the soil. Hence, SR treatment increased SHI mainly by increasing the PEO activity and NO3−–N content, and SR treatment significantly increased SHI by 25.59% and 22.16% compared with MR and DR treatments. By contrast, the DR treatment greatly increased the topsoil SHI by 43.33% and 58.98% compared with SR and SM treatments, mainly due to the enhanced microbial biomass N (MBN) and dissolved organic nitrogen (DON). The DR treatment in topsoil had the lowest soil bulk density (BD) which enhanced Bacteroidota but decreased Methylomirabilota abundance, thus resulting in the accumulation of MBN. Moreover, DR treatment led the highest maize yield which increased with an increasing SHI. To conclude, DR treatment is an effective method to improve SHI and crop productivity in nutrient‐rich topsoil, while SR treatment has a much better effect in the subsoil. Our results will provide a theoretical paradigm for selecting straw return strategies, which is crucial for promoting soil health and food productivity, achieving high crop yields, and supporting sustainable agricultural development.