A number of ecological restoration measures thus far have been implemented with the attempt to repair and reconstruct the damaged ecosystems in the northwestern arid area of China. However, there is not much available information on the effectiveness of these restoration measures. Assessment for the effectiveness of ecological restoration could serve as a reference for scientists, project designers and managers in related fields. The input grid data for our study were generated from meteorological observations of 86 stations, soil data, multi-source remote sensing images and land surface simulations. We analyzed these data with the universal soil loss equation, revised wind erosion equation, dimidiate pixel model of vegetation coverage fraction, and Carnegie Ames-Stanford Approach to estimate each index. In order to obtain more accurate indices, key land surface parameters were calibrated and localized by the observations from previous studies. Finally, a comprehensive index for the effectiveness of ecological restoration was integrated to assess the effectiveness of ecological restoration in 14 mountain-oasis-desert sub-regions in the period from 1990 to 2015. Our results showed that:(1) the ecosystem structure, quality, and functions of all investigated mountain-oasis-desert sub-systems displayed significant spatio-temporal differences. From 1990 to 2015, the ecosystem structure of the whole study area was improved, and the ecosystem quality of northern Xinjiang and Yili mountain-oasis-desert sub-system areas increased, while the ecosystem functions of the desert declined. (2) During 1990-2015, the effectiveness of the ecological restoration of the desert areas declined, but the effectiveness of ecological restoration of the oasis and mountains increased. Assessment based on the multiple indices for the effectiveness of ecological restoration could be helpful in order to objectively assess and understand the situation and dynamics of ecological restoration in the northwestern arid area of China. The results of this assessment could provide information on specific locations for future ecological restoration projects and they could be a reference for assessing the effectiveness of ecological restoration in other vulnerable regions.