Fertilization plays a crucial role in ensuring global food security and ecological balance. This study investigated the impact of substituting innovative biological manure for chemical fertilization on rice (Oryza sativa L) productivity and soil biochemical properties based on a three-year experiment. Our results suggested rice yield and straw weight were increased under manure addition treatment. Specifically, 70% of total nitrogen (N) fertilizer substituted by biological manure derived from straw, animal waste and microbiome, led to a substantial 13.6% increase in rice yield and a remarkable 34.2% boost in straw weight. In comparison to the conventional local farmer practice of applying 165 kg N ha-1, adopting 70% of total N plus biological manure demonstrated superior outcomes, particularly in enhancing yield components and spike morphology. Fertilization treatments led to elevated levels of soil microbial biomass carbon and N. However, a nuanced comparison with local practices indicated that applying biological manure alongside urea resulted in a slight reduction in N content in vegetative and economic organs, along with decreases of 10.4%, 11.2%, and 6.1% in N recovery efficiency (NRE), respectively. Prudent N management through the judicious application of partial biological manure fertilizer in rice systems could be imperative for sustaining productivity and soil fertility in southern China.