This study investigated the changes in reactor performances, microbial communities and functional genes in partial denitrification (PD) process under elevated perfluorooctane sulfonic acid (PFOS) stress. The results showed that PFOS significantly (P ≤ 0.001) decreased NO-2-N accumulation rate from 71.15 ± 1.83 % to 65.96 ± 3.97 % and increased total nitrogen removal efficiency from 25.49 ± 1.67 % to 30.90 ± 4.97 %, which indicated that PFOS addition hindered the PD process but promoted the total nitrogen removal. Excitation emission matrix fluorescence spectroscopy and fourier transform infrared spectroscopy suggested significant changes in fluorescence characteristics and functional groups of extracellular polymeric substances, especially, PFOS induced the considerable synthesis of protein-like substances. In addition, high-throughput sequencing revealed that the abundance of genus Thauera, which is responsible for the NO-2-N accumulation, was significantly decreased from 35.98 % to 26.00 % under PFOS stress. While the abundances of common denitrifying bacteria, such as genus Denitratisoma, SM1A02 and OLB8, increased after PFOS exposure, which was consistent with the changes of nitrogen transition. Moreover, PICRUSt showed that the abundance of NO-3-N reductase genes (napA) significantly (P ≤ 0.001) downregulated from 0.02 % to 0.01 %, while NO-2-N reductase genes (nirK) significantly (P ≤ 0.001) upregulated by 1.97 folds after PFOS addition. These results showed that PFOS stress had a profound influence on microbial structure and the functional genes. Overall, this study demonstrated the response mechanism of PD system to long-term PFOS stress and made some contributions to the improvement in the control strategy of wastewater treatment plants (WWTPs).