This study was conducted based on a five-year field experiment at Yixing Agro-Environment Research Base, the National Agroecosystem Observatory and Research Station of Changshu, to investigate the effects of equivalent nutrient organic fertilizer substitution and agronomic optimization on soil quality and nutrient dynamics in paddy fields, which included ten treatments: no chemical P fertilizer (CK); chemical fertilizer (CF); manures of pig (PM), chicken (CM), and cattle (DM) replacing 30% of chemical phosphorus fertilizer; biogas residues replacing 30% (OM), 50% (50%OM), and 100% (100%OM) of chemical phosphorus fertilizer; green manure incorporation (MV), and straw incorporation (ST). The results from ten crop seasons over five years revealed that, compared to CF, soil quality improved to varying degrees under organic fertilizer applications and different agronomic measures, while CK led to a 24.1% decline in soil quality over five years. Among organic fertilizer sources, PM demonstrated the most significant improvement in soil quality (16.3%); among substitution ratios, 100%OM was the most effective (18.8%); and among agronomic measures, MV achieved the highest enhancement (23.1%). Notably, the improvements in soil quality showed an increasing trend over time. Compared to the 1^st year, soil quality in the 5^th year under PM, 100%OM, and MV were promoted by 10.2, 7.17, and 2.6 times, respectively. Furthermore, soil quality index based on integrated microbial indicators (SQI-S) outperformed single physicochemical indicators in reflecting soil quality changes comprehensively, with its coefficient of variation increasing from 0.20 to 0.25, indicating greater sensitivity. In conclusion, equivalent nutrient organic substitution and optimized agronomic practices significantly enhanced paddy soil quality, providing a robust basis for sustainable soil health management.