In this study, a field experiment was conducted to reveal the characteristics of ammonia emission from traditional rice-wheat rotation (RW) and ratoon rice (RR) systems in the Taihu Lake watershed. The results showed that cumulative ammonia volatilization of RR was 74.3 kg/hm², accounting for 17.9% of total nitrogen applied. The main periods of ammonia volatilization loss were tillering fertilizer stage and regenerated tillering fertilizer stage, accounting for 31.2% and 27.0% of the total nitrogen loss, respectively. The yield, ammonia emission intensity and partial factor productivity from applied nitrogen of RR were 14.10 t/hm², 5.29 kg/t and 33.9 kg/kg. Compared with RW, ammonia volatilization accumulation, yield and nitrogen partial factor productivity of RR increased by 40.7%, 43.0% and 51.6%, respectively. In conclusion, compared to RW, RR increases ammonia emission but produces higher grain yield while with equivalent ammonia emission intensity, which suggest a great potential for ammonia volatilization reduction of RR in Taihu Lake Basin.