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Abstract As the fastest growing food production sector in the world, aquaculture may become an important source of nitrous oxide (N₂O)—a potent greenhouse gas and the dominant source of ozone-depleting substances in the stratosphere. China is the largest aquaculture producer globally; however, the magnitude of N₂O emission from Chinese aquaculture systems (CASs) has not yet been extensively investigated. Here, we quantified N₂O emission from the CASs since the Reform and Opening-up (1979–2019) at the species-, provincial-, and national-levels using annual aquaculture production data, based on nitrogen (N) levels in feed type, feed amount, feed conversion ratio, and emission factor (EF). Our estimate indicates that over the past 41 years, N₂O emission from CASs has increased approximately 25 times from 0.67 ± 0.04 GgN in 1979 to 16.69 ± 0.31 GgN in 2019. Freshwater fish farming, primarily in two provinces, namely, Guangdong and Hubei, where intensive freshwater fish farming has been adopted in the past decades, accounted for approximately 89% of this emission increase. We also calculated the EF for each species, ranging from 0.79 ± 0.23 g N₂O kg⁻¹animal to 2.41 ± 0.14 g N₂O kg⁻¹animal. The results of this study suggest that selecting low-EF species and improving feed use efficiency can help reduce aquaculture N₂O emission for building a climate-resilient sustainable aquaculture.