Satellite-based models have been widely used to estimate gross primary production (GPP) of terrestrial ecosystems. Although they have many advantages for mapping spatiotemporal variations of regional or global GPP, the performance in agroecosystems is relatively poor. In this study, a light-use-efficiency model for cropland GPP estimation, named EF-LUE, driven by remote sensing data, was developed by integrating evaporative fraction (EF) as limiting factor accounting for soil water availability. Model parameters were optimized first using CO2 flux measurements by eddy covariance system from flux tower sites, and the optimized parameters were further spatially extrapolated according to climate zones for global cropland GPP estimation in 2001–2019. The major forcing datasets include the fraction of absorbed photosynthetically active radiation (FAPAR) data from the Copernicus Global Land Service System (CGLS) GEOV2 dataset, EF from the ETMonitor model, and meteorological forcing variables from ERA5 data. The EF-LUE model was first evaluated at flux tower site-level, and the results suggested that the proposed EF-LUE model and the LUE model without using water availability limiting factor, both driven by flux tower meteorology data, explained 82% and 74% of the temporal variations of GPP across crop sites, respectively. The overall KGE increased from 0.73 to 0.83, NSE increased from 0.73 to 0.81, and RMSE decreased from 2.87 to 2.39 g C m−2 d−1 in the estimated GPP after integrating EF in the LUE model. These improvements may be largely attributed to parameters optimized for different climatic zones and incorporating water availability limiting factor expressed by EF into the light-use-efficiency model. At global scale, the verification by GPP measurements from cropland flux tower sites showed that GPP estimated by the EF-LUE model driven by ERA5 reanalysis meteorological data and EF from ETMonitor had overall the highest R2, KGE, and NSE and the smallest RMSE over the four existing GPP datasets (MOD17 GPP, revised EC-LUE GPP, GOSIF GPP and PML-V2 GPP). The global GPP from the EF-LUE model could capture the significant negative GPP anomalies during drought or heat-wave events, indicating its ability to express the impacts of the water stress on cropland GPP.