The responses of subtropical conifer plantation to climate change scenarios were investigated in Qianyanzhou by the process-based physiological-ecological model EALCO (ecological assimilation of land and climate observation). The results showed that CO2 concentration had the greatest effects on the carbon and water fluxes of the plantation, followed by temperature, and precipitation. CO2 concentration was the main driving factor for the gross photosynthesis productivity of this plantation ecosystem, and temperature and CO2 concentration were the key environmental factors controlling the ecosystem respiration. Increasing temperature accelerated the respiration of aboveground part dramatically, while increasing CO2 concentration had greater effects on soil respiration. The evapotranspiration was enhanced by increasing temperature, but reduced by increasing CO2 concentration. Under the future climate changing scenario (the year 2100), the net primary productivity of this plantation ecosystem would be increased by 22%, suggesting that this ecosystem is still capable of sequestrating carbon.