Biochar modifications are used to improve soil organic carbon (SOC) content, while its effects on soil structure stability and carbon (C) mineralization are less known especially in saline-alkaline soils. A 5 years field experiment was arranged with organic amendments addition in the Yellow River Delta, including (i) NPK, only 255, 56, and 190 kg ha-1 N, P, and K each year, (ii) RS, NPK + rice straw, (iii) BC, NPK + straw-derived biochar, and (iv) FeBC, NPK + biochar modified with ferric chloride. Relative to NPK treatment, the mean weight diameter was significantly increased with organic amendments addition, which was the highest in FeBC treatment. Meanwhile, SOC content in the soil added with organic amendment was increased by 2%-18%. Compared with the RS and BC, FeBC addition increased the content of stable humin (HU), crystalline Fe oxides (Fed), and amorphous Fe oxides (Feo). There was a positive correlation between HU and Feo/Fed, indicating HU and Fe oxides might form organic mineral complexes to limit SOC biodegradation. While the mineralization rate of SOC in FeBC treatment was decreased by more than 30.4% than that in BC treatment. This might be due to the decrease of soil beta-glucosidase and cellobiohydrolase activities, as well as the abundance of Gammaproteobacteria and Actinobacteria. These results were the mechanism of soil enzyme activity and bacterial community regulating C stability. Therefore, Fe-modified biochar is a better organic amendment to improve the stability of aggregates structure and SOC in saline-alkaline paddy soil.