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