Abstract: To investigate the effects of the co-application of medium and trace elements (magnesium, boron, zinc) along with lime on typical double-cropping rice production in South China and the improvement of acidic soils, aiming to provide a theoretical basis for regional food security and the healthy cultivation of acidic arable land. A field experiment was set up in Taishan City, one of the first key counties for acidification control, for a typical double-cropping rice planting pattern in South China, including four treatments: no fertilizer treatment (T0), conventional fertilizer treatment (T1), conventional fertilizer + magnesium&boron&zinc (T2) and conventional fertilizer + magnesium&boron&zinc + lime (T3). Grain yields, grain quality and soil acidity indicators were analyzed at rice harvesting period. Compared to T0, all fertilized treatments (T1-T3) significantly increased the early rice grain yield by 72.01%−101.54% and the late rice yield by 32.54%−61.57%, while also reducing the chalky grain rate and chalkiness of late rice and increasing the crude protein content. Compared to T1, T2 and T3 further reduced the rice gel consistency and increased the crude protein content, but the differences between T2 and T3 were not significant. Additionally, compared to T1, T2 significantly increased early and late rice grain yields by 17.16% and 21.89%, respectively, reduced the exchangeable acid content (exchangeable hydrogen and aluminum) by 9.67%, increased total exchangeable base cations (37.77%), available boron content (98.11%), and significantly increased soil pH by 0.15 units; T3 treatment significantly increased late rice grain yield by 22.24%, reduced exchangeable acid content by 79.01%, increased total exchangeable base cations (59.58%), available boron (135.84%), and available zinc (107.72%) contents, and significantly improved the soil pH by 0.44 units. The differences in grain yields between T3 and T2 treatments was not significant, but T3 treatment significantly increased total exchangeable basic cation content, available boron, and available zinc contents in the soil by 29.93%, 19.04%, and 161.97%, respectively, while reducing exchangeable acid content by 55.26% and increasing soil pH by 0.29 units. The co-application of conventional fertilizer with 150 kg∙hm⁻² magnesium sulfate, 15 kg∙hm⁻² borax and 22.5 kg∙hm⁻² zinc sulfate, as well as additional lime 1 125 kg∙hm⁻² applied together with it can maintain or promote the rice grain yield increase and effectively improve the acidic soil. The combination of conventional fertilizer, magnesium, boron, zinc, and lime showed a better effect on soil acidification improvement. However, further long-term trials are needed to validate these findings.