China is currently the leading producer and consumer of rice globally, and soil quality has a decisive impact on rice growth, including metabolite accumulation and plant disease resistance. Despite the importance of these interactions, limited research exists on the relationship between rhizosphere microorganisms and secondary metabolite profiles across different rice cultivars. To address this gap, 16s rRNA and ITS sequencing and metabolomics were used to investigate the changes in rhizosphere microorganisms and root metabolism in different rice cultivars under dryland conditions. The results showed that rice dry farming can improve soil quality by improving soil chemical properties and soil enzyme activities and increasing beneficial soil microorganisms. Compared to SLHN, the organic carbon content notably increased under dry farming, with YHSM exhibiting the highest rise at 182.90%. Soil urease (S-UE) and acid phosphatase (S-ACP) activities in YNSM also increased significantly by 116.90 and 19.65%, respectively. Additionally, rice drought farming can also increase the content of root metabolites and improve rice drought resistance. These findings offer valuable insights into the mechanism of rice under drought conditions.