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Irrigation is critical for oasis agriculture in Alar irrigated region, Northwestern China. The reference evapotranspiration (ET0) estimation using a modified Penman-Monteith method recommended by FAO is a baseline for rational irrigation scheduling. Thus, crop coefficients (Kc) were estimated using a ratio between reference and observed evapotranspiration. Then, we analyzed the relationship between temporal crop coefficients (Kc) and synchronized normalized difference vegetation index (NDVI) derived from multi-temporal remotely sensed images. The results showed that reference evapotranspiration increased from spring to summer hereafter decreased gradually to winter with the peak of ET0 ranging from 8 to 9 mm/day. A closely linear relation between NDVI and Kc of cotton was finally acquired with a coefficient of determination of 0.94. An acceptable accuracy of this model by comparing observed and simulated evapotranspiration illustrated the credibility of this model. This paper provides a scientific approach to estimate regional crop coefficient and evapotranspiration.