In order to analyze the mechanisms for promoting rice yield increase by the soil-conditioning agents(SCAs), a field experiments was carried out with SCAs (TS) and without SCAs (CK) . Exploring the improvement effect of SCAs on soil physicochemical properties by analyzing soil nutrient, and using high-throughput sequencing technology to determine the impact of application of SCAs on soil microbial community structure. Following results were obtained: After applying the SCAs(alkaline), 1) the rice yield per 667m2 increased by 54.02kg(6.83%); 2) The soil nutrient status has been significantly improved, with asignificantly increasing soil pH value and exchangeable calcium ion content; 3) The relative abundance of Geobacteraceae,Chitinophagaceae, Nitrosomonadaceae, Nitrososphaeraceae, Pleosporaceae and Ustilaginaceae was significantly increased;4) Among the top 30 families with relative abundance, Soil pH was significantly negatively correlated with the relative abundance of Chitinophagaceae, Xanthobacteraceae, Bacteroidetes_vadinHA17, Gallionellaceae and Cucurbitariaceae, and significantly positively correlated with Nitrososphaeraceae and Ustilaginaceae; The content of exchangeable calcium ions in soil was negatively correlated with the relative abundance of Xanthobacteraceae, Bacteroidetes_vadinHA17 and Terramycetaceae, and significantly positively correlated with Nitrososphaeraceae and Ustilaginaceae. These results suggestthat application of the SCAs (alkaline) can improve soil physicochemical properties and alter soil microbial structure, there by leading to enhancingaccumulation of biomass and increasing of yield of rice..