The arid desert ecosystem is very fragile, and the change of its river discharge has a direct impact on irrigation and natural environment. River discharge attenuation coefficients is a key index to reveal the stability of desert river ecosystem. However, due to the harsh conditions in desert areas, it is difficult to establish a hydrological station to obtain data and calculate the attenuation coefficients, so it is urgent to develop new methods to master the attenuation coefficients of rivers. In this study, Taklamakan desert river was selected as the research area, and the river discharge of the desert river were estimated by combining low-altitude UAV and satellite remote sensing technology, so as to calculate the attenuation status of the river in its natural state. Combined with satellite remote sensing, the surface runoff in the desert reaches of the Hotan River from 1993 to 2017 were estimated. The results showed that the base of runoff attenuation in the lower reaches of the Hotan River is 40%. Coupled UAV and satellite remote sensing technology can provide technical support for the study of surface runoff in desert rivers within ungauged basins. Using UAV and satellite remote sensing can monitor surface runoff effectively providing important reference for river discharge monitoring in ungauged catchments.