Arid and semi-arid ecosystems exhibit a spatially complex biogeophysical structure.According to arid western special climate-vegetation characters, the fractional cover of photosynthetic vegetation (PV), non-photosynthetic vegetation (NPV), bare soil and water are unmixed, using the remote sensing spectral mixture analysis. We try the method to unmix the canopy funation structure of arid land cover in order to avoid the differentiation of regional vegetation system and the disturbance of environmental background. We developed a modified production efficiency model NPP-PEM appropriate for the arid area at regional scale based on the concept of radiation use efficiency. This model refer to the GLO-PEM and CASA model was driven with remotely sensed observations, and calculates not just the conversion efficiency of absorbed photosynthetically active radiation but also the carbon fluxes that determine net primary productivity (NPP). We apply and validate the model in the Kaxger and Yarkant river basins in arid western China. The NPP of the study area in 1992 and 1998 was estimated based on the NPP-PEM model. The results show that the improved PEM model, considering the photosynthetical activation of heterogeneous functional vegetation, is in good agreement with field measurements and the existing literature. An accurate agreement (R2= 0.85, P＜0.001) between the estimates and the ground-based measurement was obtained. The spatial distribution of mountain-oasis-desert ecosystem shows an obvious heterogeneous carbon uptake. The results are applicable to add ecosystem studies ranging from characterizing carbon cycle, carbon flux over arid areas to monitoring change in mountain-oasis-desert productivity, stress and management.