Abstract: Abstract To optimize the nitrogen and phosphorus removal performance of modified pyrite coupled with PHA, an autotrophic–heterotrophic synergistic denitrification system was constructed using modified pyrite (Pyrite-S) and polyhydroxyalkanoate (PHA). The effects of influent nitrate nitrogen (NO₃^--N) concentration, total phosphorus (TP) concentration, and pH on nitrogen and phosphorus removal performance, reaction kinetics, and microbial community succession were systematically investigated. The results showed that when the influent NO₃^--N concentration was 10 mg·L⁻¹, the sulfur–carbon supply was the most balanced, the NO₃^--N removal efficiency reached ≥90%, and the reaction rate constant (k) was 0.0991 h⁻¹. When the influent TP concentration was 2 mg·L⁻¹, the “surface passivation” of the filler was alleviated, the NO₃^--N removal efficiency approached 93%, and the reaction rate constant (k) was h⁻¹. At pH 10, acidic by-products were neutralized and PHA hydrolysis was promoted, resulting in a NO₃^--N removal efficiency of ≥95% and a reaction rate constant (k) of 0.0724 h⁻¹. Microbial community analysis revealed that, through optimized regulation of NO₃^--N concentration, TP concentration, and pH, Pseudomonadota became the core functional phylum in the system, while genera such as Thiomonas, unclassified_f__Comamonadaceae, Thermomonas, Thiobacillus, and Rhodanobacter were enriched, jointly supporting the stable nitrogen and phosphorus removal performance of the system. Functional prediction further indicated that the core metabolic functions of the Pyrite-S-PHA synergistic system were chemoheterotrophy and sulfur oxidation.