Livestock manure has been widely used in agriculture to improve soil productivity and quality. However, intensive application can significantly enhance soil nitrogen (N) availability and facilitate ammonia (NH3) volatilization during rice cultivation. The effects of different rates of manure application on the NH3 volatilization rate, its mechanism, and their relationships have not been comprehensively investigated. In this study, field trials were conducted to investigate NH3 volatilization in rice paddy soils amended with different livestock manure, cattle manure (CM), and swine manure (SM), at a rate of 0 (NPK), 10, 20, and 40 Mg ha−1 during cultivation. Moreover, the soil physicochemical and biological properties and rice N uptake were investigated. Ultra-fine particulate matter (PM2.5) was measured quantitatively and qualitatively. Manure application significantly increased NH3 emissions compared to the control. Much higher volatilization rates were observed in the SM soils than in the CM soils, even when the same amount of N was applied. This is mainly related to the higher labile NH4+ concentration and urease activity in SM soils. With increasing application levels, NH3 emission rates proportionally increased in the SM, but there was no significant difference in the CM. Livestock manure application significantly increased NH3 volatilization, particularly during the initial manure application and additional fertilization stages during rice cultivation. The results showed that the application of livestock manure significantly increased NH3 volatilization. Moreover, the biochemical properties of manure composts, including labile N and urease activity, mainly affected NH3 dynamics in rice paddies during cultivation rather than their type. Irrespective of manure application, PM2.5, did not show a significant difference at the initial stage of cultivation. NH3 volatilization was not significantly correlated with the formation of PM2.5. It is necessary to develop effective strategies for mitigating NH3 volatilization and maintaining soil quality without decreasing rice productivity in paddy ecosystems.