Land-use conversion and fertilization have been widely reported as important management practices affecting CH4 and N2O fluxes; however, few long-term in situ measurements are available after land-use conversion from rice paddies to upland cultivation, especially those including the initial stages after conversion. A 3-year field experiment was conducted in rice paddies and a newly converted citrus orchard to measure CH4 and N2O fluxes in response to land-use conversion and fertilization in a red soil region of southern China. Annual CH4 and N2O emissions averaged 303.9 kg C ha-1 and 3.8 kg N ha-1, respectively, for the rice paddies over three cultivation years. Although annual N2O emissions increased two- to threefold after the conversion of rice paddies to citrus orchard, the substantial reduction in CH4 emissions and even shift into a sink for atmospheric CH4 led to significantly lower CO2-eq emissions of CH4 and N2O in the citrus orchard compared to the rice paddies. Moreover, distinct CH4 emissions were observed during the initial stages and sustained for several weeks after conversion. Our results indicated that the conversion of rice paddies to citrus orchards in this region for higher economic benefits may also lead to lower aggregate CH4 and N2O emissions.