The study of the effects of different fertilization treatments on soil methane (CH4) and nitrous oxide (N2O) emissions in rice-vegetable rotation systems is of great significance to supplement the research gap on greenhouse gas emissions in tropical regions of China. In this study, four fertilization treatments were set up during the pepper season:phosphorus and potassium fertilizer application (PK); nitrogen, phosphorus, and potassium (NPK) application; half application of nitrogen, phosphorus, and potassium plus half application of organic fertilizer (NPK+M); and application of organic fertilizer (M). There was no fertilizer application during the following early rice season. The objective of our study was to investigate the rules of CH4 and N2O emissions under different fertilization treatments in the pepper growth season, and the effects of different fertilization treatments in the pepper growth season on rice yield, and CH4 and N2O emissions in the following early rice growth season. The close static chamber-gas chromatography method was applied to determine soil CH4 and N2O emissions. We measured crop yield, estimated global warming potential (GWP), and calculated greenhouse gas emission intensity (GHGI). Our results showed that:① the cumulative CH4 emission under the four fertilization treatments ranged between 0.9 kg·hm-2 to 2.7 kg·hm-2 during the pepper growth season and between 5.5 kg·hm-2 to 8.4 kg·hm-2 during the early rice growth season. Compared with NPK, NPK+M and M reduced the cumulative CH4 emission in the pepper growth season by 35.3% and 7.6%, respectively; however, NPK+M and M increased the cumulative CH4 emission in the early rice season by 37.5% and 55.1%, respectively. There was a significant difference in cumulative CH4 emission between M and NPK in the early rice growth season. ② The cumulative N2O emission under the four fertilization treatments varied from 0.5 kg·hm-2 to 3.0 kg·hm-2 in the pepper growth season and from 0.3 kg·hm-2 to 0.5 kg·hm-2 in the early rice growth season. The cumulative N2O emission was significantly decreased by 33.7% in NPK+M and by 16.0% in M, compared with that in NPK. In the early rice growth season, the cumulative N2O emission was decreased by 23.5% by NPK+M but was increased by 9.1% by M. There was no significant difference in the cumulative N2O emission among the four fertilization treatments. ③ The yields of pepper and early rice under the four fertilization treatments were 3055.6-37722.5 kg·hm-2 and 5850.9-6994.4 kg·hm-2, respectively. Compared with that in NPK, NPK+M and M significantly increased pepper yield. The GWP under the four fertilization treatments in the pepper-early rice rotation system varied from 508.0 kg·hm-2 to 1864.4 kg·hm-2. Compared with NPK, NPK+M significantly decreased GWP by 25.7% and M insignificantly decreased GWP by 5.7%. The pepper growth season with the four fertilization treatments contributed to 69.2%-78.1% of the total GWP, and N2O contributed to 77.3%-85.3% of the total GWP. The GHGI ranged between 0.03 kg·kg-1 and 0.09 kg·kg-1 in the pepper growth season and between 0.04 kg·kg-1 and 0.24 kg·kg-1 in the early rice growth season. Compared with that in NPK, both M and NPK+M significantly reduced the GHGI by 71.5% and 54.7%, respectively, in the pepper growth season. In the early rice season, NPK+M significantly decreased the GHGI by 44.0%, but M non-significantly decreased the GHGI by 20.8%. The peak in N2O emission in the tropical pepper-early rice rotation system appeared after fertilization, and N2O emissions primarily occurred in the pepper growth season. However, CH4 emission was mainly concentrated in the early rice season. Considering the overall enhancing effects on crop yield and mitigation of greenhouse gas emissions, the co-application of chemical and organic fertilizers (NPK+M) can be recommended as an optimal fertilization practice to mitigate greenhouse gas emissions and maintain crop yield in pepper-rice rotation systems of Hainan, China.