Rice ratooning produces a second harvest from the growth of axillary buds that remain on the stubble after the main crop is harvested. Stubble rolling after mechanical harvesting may regenerate roots and tillers. The objective of this study was to elucidate the relationships between axillary bud regeneration and yield formation in ratoon rice. The experimental approach was to measure yield and axillary bud regeneration traits under full-rolling and non-rolling treatments across three sites in Fujian Province, China over two years. Full-rolling increased grain yield by 7.59%–8.40% and the regeneration capacity of axillary buds by 9.45%–17.11%. Further analyses revealed that full-rolling increased the activities of carbon- and nitrogen-metabolizing enzymes in regenerating axillary buds, as well as the expression of genes involved in carbohydrate and nitrogen metabolic pathways. Mechanical harvesting combined with stubble rolling that presses rice stubble close to the soil surface induces a regenerative growth pattern that ultimately increases ratoon rice yield.