Bamboo forests are widely distributed in the tropical and sub-tropical regions, and have a great carbon sequestration capacity. However, the carbon dynamics of bamboo forest are still poorly understood. This study developed an algorithm for assimilating LAI dynamics based on an integrated ensemble Kalman filter using MODIS LAI data, MODIS reflectance data, and canopy reflectance data modeled by PROSAIL for two typical bamboo forests. The assimilated LAI was highly consistent with the observed LAI, yielding correlation coefficient (r) of 0.84 and 0.94 for Moso bamboo forest and Lei bamboo forest, respectively. Then, the spatiotemporal pattern of the CO2 fluxes within bamboo forest were modeled for Zhejiang Province during 2011–2014 using the Boreal Ecosystem Productivity Simulator model driven by assimilated LAI. The modeled CO2 fluxes were in agreement with the CO2 fluxes measured by eddy covariance technology at two selected sites within the study region. Average r, absolute deviation, and root mean square error values were 0.77, 0.65gCm−2day−1, and 0.82gCm−2day−1, respectively. Bamboo stands with high Net Ecosystem Exchange (NEE) values were found to be distributed throughout mountainous areas in the northwest, southwest, and northeast of Zhejiang, while low NEE stands were located in the mountain basin areas, high altitude areas, and the majority of coastal areas. Among the eleven cities in Zhejiang Province, Hangzhou was the highest annual total NEE city (0.34±0.06TgCyr−1), and Huzhou was the highest NEE density city (7.65±1.02MgChm−2yr−1). The carbon sequestrated by bamboo forest was 1.74TgCyr−1, accounted 6.36Tg CO2 yr−1, which indicated the bamboo forested area in Zhejiang Province was a carbon sink. The spatial heterogeneity of CO2 fluxes of bamboo forest can be revealed by an exponential semivariance model. The analysis of the model structure indicated that the spatial heterogeneity of CO2 fluxes of bamboo forest was characterized by significant autocorrelation, with an average autocorrelation range of 3.00km, however the effect of random factors (management levels, management measures, etc.) cannot be ignored. This is the first time that the CO2 fluxes of bamboo forest in Zhejiang Province have been mapped and this study provides a new estimate of CO2 fluxes in this region.