This study addressed the challenges of low efficiency and operational instability in decentralized flush toilet waste management in rural areas of Heilongjiang, a cold region in China. By introducing a microbial composite agent, we aimed to enhance the stability and quality of effluent. Through long-term monitoring of flush toilets in rural households, we analyzed the water quality changes in the treatment of "black water" and "gray water", focusing on parameters such as chemical oxygen demand (COD), ammonia nitrogen (NH₃-N), total nitrogen (TN), total phosphorus (TP), and fecal coliform content. The results showed that during black water treatment, COD removal rates reached as high as 91.53%, with ammonia nitrogen removal consistently above 80%, and total phosphorus removal rate fluctuating between 63.85% and 82.00%. In gray water treatment, COD removal rates ranged from 81.95% to 90.08%, and ammonia nitrogen removal peaked at 91.11%. Additionally, the composite agent significantly reduced fecal coliform counts in the effluent, achieving a removal rate over 90%. Bacterial community structure analysis revealed that the application of the composite agent optimized microbial composition, effectively enriching cold-tolerant microbes such asAcinetobacterandPsychrobacter. This study demonstrated that the use of microbial composite agents in rural toilet waste treatment in cold regions not only improved pollutant removal efficiency and operational stability but also provided a scientific basis and technical support for the renovation of rural toilets and fecal waste management in cold regions.