ABSTRACT Although diversified crop rotations increase drought tolerance and system productivity, the underlying mechanisms conferring this resilience in crop–soil–microorganisms systems remain incomplete. Maize drought tolerance mechanisms were evaluated in a 20‐year experiment with low, medium, and high crop diversity rotations using soil zymography to visualize enzyme activity distribution and high‐throughput sequencing to assess microbial communities. High crop diversity increased maize shoot biomass by 56%–87% and reduced drought‐induced root biomass loss by 14%–59% compared to low crop diversity. Root diameter increased by 1.7–2.5 times leading to better drought tolerance by 2.2–2.7 times, and stabile key rhizosphere microbiota. The complexity of the rhizosphere bacterial network increased with crop diversification, and the keystone taxa (such as biofilm‐producing Pseudomonas ) raised maize drought tolerance by increasing rhizosphere water retention. These microbiota increased habitat resilience under drought, increasing ecosystem provision and regulatory functions. Activities and hotspot areas of enzymes related to carbon and nitrogen cycling decreased with crop diversification, but changed minimally under drought, indicating that this enzymatic resilience could contribute to maize drought tolerance. In conclusion, crop diversification enriches drought‐tolerance microbial species in soil that stabilize the rhizosphere microenvironment and facilitate root proliferation, underscoring the importance of crop–microbial interactions for drought resilience.