With large area of primary tropical rainforest converted into rubber (Hevea brasiliensis) plantation in Southeast Asia, it is necessary to examine the change in soil CO2 and CH4 emissions, and their underlying drivers in tropical rainforest (TRF) and rubber plantation. In TRF and RP in Xishuangbanna Southwest China, we measured the soil CO2 , CH4 , temperature, and water content once each week from 2003 to 2008, and twice weeks in 2013 and 2014. Additionally, the concentrations of soil carbon (C) and nitrogen (N) fractions from 2013 to 2014 were observed. Inputs of litter and live, dead, decomposed fine roots dynamics were also included. TRF transplanted to RP did not change significantly the annual soil CO2 emissions (TRF, 359 ± 91 and RP 352 ± 41 mg CO2 m−2 h−1) but decreased soil CH4 uptake significantly (TRF, −0.11 ± 0.18 mg CH4 m−2 h−1) RP, −0.020 ± 0.087 mg CH4 m−2 h−1). The most important influence on soil CO2 and CH4 emissions in the RP was the leaf area index and soil water content, respectively, whereas the soil water content, soil temperature, and dead fine roots were the most important factors in the TRF. Variations in the soil CO2 and CH4 caused by land-use transition were individually explained by soil temperature and fine root growth and decomposition, respectively. The results show that land-use change varied the soil CH4 and CO2 emission dynamics and drivers by the variation of soil environmental and plant's factors.