Ridge tillage at two fertilizer depths is a new type of conservation tillage method that was previously shown to substantially improve rice yield. This study aimed to compare the effects of continuous ridge tillage at two fertilizer depths (L treatment) with those of conventional cultivation (P treatment) on bacterial and fungal diversity in the rice root zone and study the correlation between microorganisms and yield components. At the mature stage, the yield and yield components of rice plants were compared. Test soil (0–20 cm) with continuous tillage for 3 years was used for high-throughput sequencing to analyze the microbial community structure in the root–soil of the two treatments. We found that the L treatment increased soil nutrient content and improved soil physical properties, which altered the composition of the microbial community. The bacterial ACE and Chao indices in the L treatment increased by 1.46% and 1.83%, respectively, and the fungal ACE and Chao indices increased by 5.25% and 5.49%, compared with the P treatment, respectively. The average theoretical yield under the L treatment was 9781.51 kg/ha, which was 19.23% higher than that under the P treatment. Continuous ridge tillage at two fertilizer depths can provide a better soil environment for rice growth and increase the yield.