Aquaculture is a major source of greenhouse gas emissions, yet long-term spatiotemporal variations of emissions remain poorly documented. Here, we studied methane and nitrous oxide emissions from aquatic environments and carbon dioxide emissions from fishing vessel fuel combustion of the China's aquaculture industry between 2000 and 2020. Results show that greenhouse gas emissions from aquaculture increased from 183.1 to 203.3 Tg of CO2-equivalent from 2000 to 2020, exhibiting a wave growth pattern. Spatiotemporal patterns show that China's top six provincial greenhouse gas emitters, namely Hubei, Jiangsu, Zhejiang, Anhui, Hunan, and Sichuan, collectively released 98.5 Tg, accounting for 45% of the country's total aquacultural greenhouse gas emissions. Also, we find that six provinces, namely Hubei, Anhui, Hunan, Jilin, Liaoning, and Jiangxi, present high emission growth rates ranging from 46.9 to 154% between 2000 and 2020. Moreover, methane emissions from extensive and semi-intensive freshwater aquaculture production contribute 90.7% of China's total aquaculture greenhouse gas emissions, thus dominating the sector's greenhouse gas emissions. Our findings highlight the need to reduce emissions in provinces with high aquaculture greenhouse gas emissions or growth rates, with a focus on methane reduction from freshwater aquaculture.