With the increase of tree plantation areas, how to evaluate accurately their carbon storage and sequestration is significant for estimating global or regional carbon balance. Process-based ecosystem models provide a realistic approach to analyze and predict the dynamic of C storage and fluxes after afforestation. CEVSA2 is a new version of CEVSA with improvements on some key processes of carbon and water cycles. CEVSA2 model was validated and calibrated by eddy flux data in 2003 and 2004 at Qianyanzhou station. The study site is one of the ‘ChinaFlux network’ and located in South China subtropical monsoon climatic zone. After the native vegetation, subtropical evergreen broad-leaved forest, was degraded after a long disturbance, the vegetation was dominated by grass and shrub after 1950s, and then the coniferous plantation has been established since 1983. Based on CEVSA2, we simulated simulated the change of carbon fluxes and storage in grass from 1951 to 1982, and then forest from 1983 to 2004. Based on the CEVSA2 model simulations, we analyzed the change of carbon fluxes and storage of coniferous plantation after afforestation in 1983. The results showed that vegetation C increased at a rate of 22% after afforestation. The soil C decreased in the first 7 to 8 year after planting, and then increased gradually. Soil carbon was equal to the initial value 15 year later. Ecosystem total carbon storage also decreased in the early period after afforestation, and then increased with the growth. Total carbon storage shifted from decreasing to increasing trend in the 4th year after planting, and exceeded the initial value in the 6th year after planting. Gross and net primary productivity increased with the growth. Total ecosystem respiration decreased firstly and then increased. Autotrophic respiration ratio of total respiration increased with growth, and heterotrophic respiration ratio was decreased inversely. All these results showed that the total carbon storage decreased, and ecosystem released carbon to atmosphere during the early period of afforestation. With the growth of forest, ecosystem became a carbon sink, and vegetation, soil and total carbon storage increased obviously.