Gypsum application can significantly increase the productivity of soda saline-alkaline paddy fields, primarily due to its strong effects on soil organic carbon (C) content. However, despite their importance, the specific mechanisms by which gypsum influences the dynamics and composition of soil organic C in soda saline-alkaline paddy fields remain largely unexplored. Therefore, in a paddy field converted from newly reclaimed saline-alkali wasteland, we conducted an experiment with four gypsum amendment treatments: 0 t/ha (CK), 15 t/ha (G 15), 30 t/ha (G 30), and 45 t/ha (G 45). We investigated the effects of gypsum application rate on soil organic C and bacterial communities in the soda saline-alkaline paddy field and explored how soil bacteria affected organic C. Compared with CK, G 30 significantly reduced soil pH by 14.42% and total dissolved salts (TDS) by 23.85%. In G 45, particulate organic C and mineral-associated organic C contents were 1.08 g/kg and 15.06 g/kg, respectively, which were significantly higher by 556.83% and 77.70%, respectively, than those in CK. The dissolved organic C content in G 30 was 0.05 g/kg, which was significantly lower by 72.22% than that in CK. Regarding soil biological activity, compared with CK, activities of β-1,4-glucosidase (0.54 nmol/h/g) and β-fibrous diglucosidase (96.25 nmol/h/g) increased significantly in G 45. In G 30, compared with CK, activities of β-xylosidase (32.23 nmol/h/g) and α-glucosidase (62.97 nmol/h/g) increased significantly. The Shannon and Observed_species alpha diversity indices of the bacterial community in G 30 increased significantly by 36.31% and 16.10%, respectively, compared with that in CK. The copy number of functional genes involved in methane metabolism, carbon fixation, and carbohydrate metabolism in G 30 increased by 2.92% to 8.86% compared with that in CK. Partial least squares path analysis indicated that gypsum application increased bacterial accumulation of organic C by improving the environment for soil bacteria with reductions in soil pH and HCO 3 –+CO 3 2– content in soda saline-alkaline paddy fields. The findings of this study support refining the theoretical framework by which gypsum amendments improve soda saline-alkaline soils.