Abstract: To understand the emission rules and influencing factors of ammonia volatilization (NH₃) and greenhouse gases (N₂O, CH₄, and CO₂) in paddy fields, where organic fertilizer replaces chemical fertilizer under a rice-duck symbiosis system in the Erhai Lake Basin, we conducted a randomized block field experiment. The experiment used the ‘Yungeng 37’ rice variety and dry ducks as experimental subjects, with an equal nitrogen input of 180 kg·hm⁻². Four treatments were established: 1) rice monocropping with no fertilizer and ducks (CK), 2) cattle manure replacing chemical fertilizer in rice-duck symbiosis system (C+D), 3) chicken manure replacing chemical fertilizer in rice-duck symbiosis system (P+D), and 4) chemical fertilizer in rice-duck symbiosis system (F+D). Ammonia volatilization and greenhouse gas emissions from paddy fields were monitored after each fertilization, and pH, Eh, and contents of NH₄⁺-N and NO₃⁻-N in the soil and surface water were measured. The results showed that ammonia volatilization rate peaked at 1−4 days post-fertilization. Compared with the F+D treatment, replacing chemical fertilizer with organic fertilizers in the rice-duck symbiosis system significantly reduced the ammonia volatilization rate of the paddy field by 56.41%–87.05%, decreased the accumulation of ammonia volatilization by 95.47%–98.65%, and lowered volatilization loss rate by 96.00%–99.22%. There was no significant difference in cumulative ammonia volatilization between the C+D and P+D treatments. Replacing chemical fertilizer with organic fertilizer in a rice-duck symbiosis system significantly reduced N₂O emission flux by 56.71%–56.93%, cumulative N₂O emissions by 70.36%–70.52%, and cumulative CO₂ emissions by 10.49%–30.54%. However, it significantly increased CH₄ emission flux by 136.56%–182.34%, and CH₄ cumulative emission by 61.96%–93.33%. There was no significant difference in the global warming potential (GWP) and greenhouse gas intensity (GHGI) between the rice-duck symbiosis system using organic fertilizer and the F+D treatment. The main factors affecting ammonia volatilization were the concentrations of nitrogen, total dissolved nitrogen, NH₄⁺-N, and NO₃⁻-N in the surface water. The main factors affecting greenhouse gas emissions were soil temperature, pH, Eh, contents of NH₄⁺-N and NO₃⁻-N, and rainfall. Under the rice-duck symbiosis system, replacing chemical fertilizer with organic fertilizer can significantly reduce ammonia volatilization and N₂O emissions. Additionally, using chicken manure instead of chemical fertilizers can significantly increase rice yield, making it a sustainable development measure for reducing emissions, increasing efficiency, and stabilizing yield.