Excessive use of chemical fertilizers negatively impacts crop productivity and farmland ecosystem, impeding sustainable agricultural progress. Consequently, there is an immediate need for a chemical fertilizer reduction strategy that ensures crop productivity and improves soil quality and the ecological environment of farmland. This study implemented a three-year (2018–2020) field experiment with two chemical fertilizer reduction methods (direct fertilizer reduction and organic substitution) to investigate their effects on wheat productivity, soil quality, heavy metal pollution risk and microbial characteristics. The results showed that organic substitution treatments (OF1, OF2 and OF3) improved most wheat plant (nutrient uptake and yield and its components) and soil properties (soil nutrients and carbon and nitrogen fractions), leading to increased crop productivity index (CPI, by 9.18 %-16.39 % and 14.14 %-23.36 %) and soil quality index (SQI, by 84.67 %-138.86 % and 104.11 %-175.91 %) compared to conventional fertilization (CF) and direct fertilizer reduction treatments (RF1, RF2 and RF3) in 2019 and 2020. Additionally, organic substitution enhanced the diversity and network complexity of bacterial community, while raising the soil pollution index (SPI, by 9.30 %-12.84 % and 12.20 %-18.49 %) without causing soil heavy metal pollution. Thus, it is recommended to adopt organic fertilizer substitution as the primary chemical fertilizer reduction strategy for wheat production. This approach will ensure crop yield, and improve soil quality and microbial characteristics, but its long-term application requires monitoring changes in soil heavy metals. Overall, this study provides guidelines for implementing scientific fertilization in agricultural practices, thus contributing to the health and sustainability of farmland ecosystems.