Abstract: Soil acidification constrains the rice production potential in South China. This study explored the effects of straw returning combined with lime application in ameliorating acidic soils, aiming to provide a practical basis for improving desilicated and aluminum-rich acidic soils in South China. A double-rice (early and late season) field experiment was conducted with four treatments: conventional fertilization (CF), conventional fertilization + quicklime (CFL), conventional fertilization + straw returning (CFS), and conventional fertilization + straw returning + quicklime (CFSL). The rice yield, soil physicochemical properties, organic carbon fractions, enzyme activities, and microbial community structure were systematically measured. The results showed that compared with CF, CFSL increased rice yield by 2.22%−29.57%. For soil acidification indicators, both CFL and CFSL significantly reduced exchangeable acidity and exchangeable aluminum content, while significantly increasing soil pH value by 0.60 and 0.36, respectively. In addition, CFS and CFSL significantly increased soil cation exchange capacity (CEC) by 17.72% and 20.58%, respectively. In terms of soil organic carbon, compared with CF, CFSL increased microbial biomass carbon and dissolved organic carbon content by 26.53% and 34.20%, respectively. Concurrently, CFSL enhanced the activities of soil urease, β-glucosidase, and sucrase by 33.60%, 19.49%, and 13.89%, respectively. Microbial community structure analysis further revealed that CFSL not only increased the relative abundance of the bacterial phylum Proteobacteria but also significantly enhanced fungal alpha diversity and drove a pronounced “trade-off” in abundance between Ascomycota and Basidiomycota, thereby reshaping the composition and functional profile of the microbial community. In conclusion, straw returning combined with lime application optimizes the chemical properties and microbial community structure of acidic soils, effectively alleviated soil acidification, and promoted stable and increased rice yields, providing an efficient and feasible technical approach for ameliorating acidic soils in South China.