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Nanoplastics are widely distributed in the environment and can accumulate in organisms. Increasing attention has been paid to the toxic effects of nanoplastics in wastewater biological treatment processes. In this study, polystyrene nanoplastics with different charges were synthesized and used in sequencing batch activated sludge reactors for short-term nanoplastic exposure experiments. Both positively and negatively charged nanoplastics inhibited the nitrogen removal efficiency and gene expressions of nitrification and denitrification-related genes of activated sludge. The inhibiting effect on nitrification of both nanoplastics was enhanced with increasing concentration. The study further evaluated the molecular mechanisms by which differently charged nanoplastics affect denitrification efficiency using the model denitrifying bacterium Pseudomonas stutzeri （ P. stutzeri ） . The results showed that both positively and negatively charged nanoplastics affected the efficiency of biological denitrification by P. stutzeri , mainly including the promotion of NO 3 - to NO 2 - conversion and the significant acceleration of N 2 O production. Meanwhile, negatively charged nanoplastics inhibited the growth of P. stutzeri and disrupted the cell membrane of the bacterium； however, no change was observed in the expression of denitrification-related functional genes and the nanoplastics might have affected the enzymatic activities of Nir and Nos, which in turn affected the bioprocessing efficiency. This study can provide a certain reference for the evaluation of the biosafety of nanoplastics and provide a certain support for the stable operation of wastewater treatment plants.