Estimates of regional net primary productivity (NPP) are useful in modeling regional and global carbon cycles, especially in karst areas. This work developed a new method to study NPP characteristics and changes in Chongqing, a typical karst area. To estimate NPP accurately, the model which integrated an ecosystem process model (CEVSA) with a light use efficiency model (GLOPEM) called GLOPEM-CEVSA was applied. The fraction of photosynthetically active radiation (fPAR) was derived from remote sensing data inversion based on moderate resolution imaging spectroradiometer atmospheric and land products. Validation analyses showed that the PAR and NPP values, which were simulated by the model, matched the observed data well. The values of other relevant NPP models, as well as the MOD17A3 NPP products (NPP MOD17), were compared. In terms of spatial distribution, NPP decreased from northeast to southwest in the Chongqing region. The annual average NPP in the study area was approximately 534 gC/m2a (Std. = 175.53) from 2001 to 2011, with obvious seasonal variation characteristics. The NPP from April to October accounted for 80.1% of the annual NPP, while that from June to August accounted for 43.2%. NPP changed with the fraction of absorbed PAR, and NPP was also significantly correlated to precipitation and temperature at monthly temporal scales, and showed stronger sensitivity to interannual variation in temperature.