Temporal variation is a major source of the uncertainty in estimating the fluxes of the greenhouse gases (GHGs) in terrestrial ecosystems, and the GHG fluxes and its affecting factors in the karst region of southwest China remains weakly understood. Using the static chamber technique and gas chromatography method, the CO2, CH4 and N2O fluxes were carried out between 9 and 11 a.m. at 15 day intervals from June 2008 to May 2009 in a Pinus massoniana forest. Two treatments were chosen for this study: undisturbed (soil with litter layer) and disturbed (surface litter removal). Both treatments were found to be the net source of atmospheric CO2 and N2O, but a sink of atmospheric CH4. The seasonality of soil CO2 emission coincided with the seasonal climate pattern, with high CO2 emission rates in the hot-wet season and low rates in the cool-dry season. In contrast, seasonal patterns of CH4 and N2O fluxes were not clear, although higher CH4 uptake rates were often observed in autumn and higher N2O emission rates were often observed in spring (dry-wet season transition). The litter was active in GHG fluxes, and removal of the litter layer reduced soil CO2 emission (17%) and increased CH4 uptake (24%) whereas N2O fluxes were not affected distinctly in the pine forest, indicating that litter layer had an important effect on C exchanges. In the pine forest, soil CO2 emissions and CH4 uptakes correlated significantly with soil temperature (r2 = 0.87, P <0.01; r2 = 0.34, P <0.05, respectively), but had no significant relationship with soil moisture. And there was a significant correlation between CH4 flux and NH4+-N (r2 = 0.39, P < 0.05) and soil inorganic N (r2 = 0.48, P <0.05), but no significant correlation was found between CH4 flux and NO3--N. Moreover, we found a significant negative logarithmic correlation between N2O flux and soil NO3--N concentration (r2 = 0.41, P <0.05), and the relationship between CO2 emission and soil inorganic N content (r2 = 0.35, P < 0.05). These results suggested that soil temperature and mineral N dynamics largely affected the temporal GHG exchanges between forest soil and atmosphere.