<p>Sulfur autotrophic denitrification (SAD) is a promising biological nitrogen removal technology without CO₂ emissions. However, the impact of seasonal temperature variations on SAD performance, especially in the treatment of actual municipal secondary effluent, remains unclear. To address this issue, a composite substrate SAD reactor (i.e., SPSAD), where element S⁰ and pyrite (v:v/1:3) were uniformly mixed in hollow plastic balls that served as the filler, was developed in this paper. The performance of the SPSAD reactor was comprehensively evaluated under 190 d of seasonal variation. The results indicated that the nitrate removal loading (NRL), nitrate removal efficiency (NRE), and PO₄³⁻-P removal rate decreased from 0.060 kg NO₃⁻-N /(m³·d), 93.2% and 67.9% to 0.032 kg NO₃⁻-N /(m³·d), 49.9% and 30.2%, respectively, when the temperature decreased from 35 °C to 9 °C. The SPSAD reactor was effective at performing denitrification under temperature variations. Additionally, the ratio of ΔSO₄²⁻ to ΔNO₃⁻-N gradually decreased from 6.48 to 5.34 as the temperature decreased, revealing a shift in the predominant electron donor for denitrification from S⁰ to pyrite. Microbial analysis revealed that the average abundance of <i>Proteobacteria</i> was 53.11%, making it the dominant phylum in the reactor. <i>Thiobacillus</i> was significantly enriched as the predominant genus responsible for denitrification, with its abundance decreasing from 33.2% at Stage I (25–35 °C) to 26.4% at Stage III (9–11 °C). The feasibility and advantages of NO₃⁻-N and PO₄³⁻-P removal via the SPSAD reactor were discussed and demonstrated in practical applications. This study provides stakeholders with scientific support for the deep treatment of municipal secondary effluent in cold areas.</p>