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Atmospheric ammonia (NH3) can affect nitrogen deposition, particle acidity, and gas-particle partitioning. Although the inorganic chemistry of NH3 in fine particulate (PM2.5) formation are well-constrained, the understanding of interactions between NH3 and secondary organic aerosol (SOA) are rather insufficient until recently. Laboratory studies indicate that NH3 molecule can react with SOA then forms nitrogen-containing organic compounds (NOCs), which can further react to form heterocyclic organic compounds. In this study, we use a modified version of the CMAQ model to simulate the potential importance of the SOA-ammonia uptake mechanism on air quality over China in summer and winter 2017, considering a range of assumed NH3 uptake coefficients (10−3–10−5). Our results show that uptake of NH3 by SOA leads to a decrease in gas-phase NH3 mixing ratio, by as much as 27.5% and 19.0% for the highest uptake coefficient scenario (10−3) in summer and winter, respectively. The largest reduction of ammonia occurs over the Sichuan Basin and the North China Plain. The reduction of gas-phase NH3 engenders a decrease of ammonium nitrate, by up to 30%, but has little impact on the ammonium sulfate concentration. Uptake of NH3 does not significantly affect SOA concentrations owing to overall moderate changes in aerosol acidity, and thus small effects on SOA formation from isoprene. Altogether, NH3 uptake led to a reduction in the average PM2.5 concentration up to 8.9% and 8.7% for the highest uptake coefficient (10−3) in summer and winter, respectively. These results highlight the need for better constraints on the NH3-SOA interactions.