Organic improvement measures play a crucial role in the reclamation of saline‐sodic soil. However, there is still a limited understanding regarding the relationships between soil microbes and soil properties and crop yield in response to the application of these organic materials to saline‐sodic soils. In a field trial, the following treatments were carried out: no modifier input (CK) and compound lignite organic modifier 30 t/ha (LOM) with 2 years of rice cultivation, no modifier input (RF) with 5 years of rice cultivation, and the full amount of straw was returned to the field with rice‐duck farming (SW). Compared with RF and CK, the SOM content in the 0–20 cm soil layer of SW and LOM was significantly increased by 4.600 and 5.020 g kg−1, respectively, while the total alkalinity and pH were significantly decreased. In the 20–40 cm soil layer, the LOM treatment resulted in decreased pH and total alkalinity compared with other treatments. Overall, changes in soil microbial structure changes were significantly associated with SOM and pH levels. In the 0–20 cm soil layer, the LOM treatment significantly increased the relative abundance of Proteobacteria, while SW treatment significantly increased the relative abundance of Bacteroidetes and Firmicutes compared with CK. Moreover,the relative abundances of Longobacteriaceae of Bacteroidetes, Hydrogenaceae, and Xanthomonas of Proteobacteria were positively correlated with crop yield. The yields of SW and LOM were 6985.587 and 7879.910 kg ha−1, respectively. These results demonstrate that implementing comprehensive organic improvement measures can enhance the properties of saline‐sodic soil and increase crop yield, with lignite composite organic amendments may be more suitable for sustainable agricultural development.