Abstract: This study investigated the effects of the co-application of medium and trace elements (magnesium, boron, and zinc) with lime on typical double-cropping rice production and acidic soil improvement in South China, aiming to provide a theoretical basis for regional food security and healthy cultivation of acidic arable land. A field experiment for a typical double-cropping rice system was set up in Taishan City, Jiangmen City of Guangdong Province in South China, one of the first key counties for national soil acidification control, including four treatments: no fertilization treatment (T0), conventional fertilization treatment by farmers (T1), conventional fertilization + magnesium & boron & zinc treatment (T2), and conventional fertilization + magnesium & boron & zinc + lime treatment (T3). Grain yield and grain quality of both early and late rices, and soil acidity indicators of late rice were analyzed during the rice harvesting period. Compared to T0 treatment, all fertilization treatments (T1, T2, and T3) significantly increased the early rice grain yield by 72.02%−101.54% and the late rice yield by 32.55%−62.03%, while also reduced the chalky grain rate and chalkiness, and increased crude protein content of late rice. Compared to T1 treatment, T2 and T3 treatments further significantly reduced the rice gel consistency and increased the crude protein content, while the differences of crude protein content between T2 and T3 were not significant. Additionally, compared to T1 treatment, the T2 treatment significantly increased early and late rice grain yields by 17.16% and 21.90%, respectively, reduced the exchangeable acid content (exchangeable hydrogen and aluminum) by 9.67%, significantly increased total exchangeable base cations content by 37.77%, significantly increased available boron content by 98.11%, and significantly increased soil pH by 0.15 units; T3 treatment significantly increased late rice grain yield by 22.24%, significantly reduced exchangeable acid content by 59.58%, significantly increased total exchangeable base cations content by 79.01%, and significantly increased available boron and zinc contents by 135.84% and 167.72%, respectively. Additionally, T3 treatment significantly increased soil pH by 0.44 units compared to T1 treatment. The differences in grain yields between the T3 and T2 treatments were not significant. However, compared to T2 treatment, T3 treatment significantly increased the total exchangeable basic cations content, available boron content, and available zinc content in the soil by 29.93%, 19.04%, and 161.97%, respectively, while significantly reduced the exchangeable acid content by 55.26% and significantly increased the 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, along with 1 125 kg∙hm⁻² lime, can sustain or enhance rice grain yield and effectively ameliorate acidic soils. The combination of conventional fertilizers with magnesium, boron, zinc, and lime showed the best effect on soil acidification. However, long-term trials are required to validate these findings.