In order to analyze the mechanisms for promoting rice yield by the soil-conditioning agents(SCAs)，a field experiment was carried out，and treatments with SCAs (TS) and without SCAs (CS) were conducted . The improvement effect of SCAs on soil physicochemical properties was explored by analyzing soil nutrient，and high-throughput sequencing technology was used to determine the impact of application of SCAs on soil microbial community structure. The results showed that，after applying the SCAs(alkaline)，(1)the rice yield increased by 810.15 k·hm-2(6.83%)；(2)The soil nutrient status was significantly improved，with a significantly 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 suggested that application of the SCAs (alkaline)could improve soil physicochemical properties and alter soil microbial structure，thereby leading to the enhancing accumulation of biomass and increasing of yield of rice.