Long-term rotations of green manure crops in acidic paddy soil can improve soil quality, crop yield sustainability, and nutrient balances in a rice-based cropping system. Different green manure rotations increased grain yield and sustainable yield index compared to a control treatment. Green manure also enhanced soil chemical properties like organic matter and nitrogen levels. However, it did not prevent soil acidification from inorganic fertilizers. Enzyme activities like phosphatase and urease were boosted by green manure, while nitrogen and phosphorus balances were reduced. Soil properties, cropping systems, and climate factors all played a role in annual grain yield. Overall, green manure rotations are beneficial for maintaining high crop yields by enhancing soil quality and reducing nutrient imbalances in acidic soil under double-rice cropping systems.