The Tarim River is an important inland river with simple species composition and nutrient structure in southern Xinjiang, China. In the past few decades, with the intensification of human activities, the intensity of the water resources development and use has increased, seriously squeezing the ecological water consumption. As a consequence, the river stopped flowing and the vegetation of the desert riparian forests in the lower reaches of Tarim River decayed. To save the seriously declining desert riparian forests, an ecological water conveyance project has been carried out in the lower reaches of Tarim River since 2000. However, the status of ecosystem resilience after water conveyance has not been deeply and systematically studied yet. Ecological resilience refers to the ability of an ecosystem to restore itself to its pre-damaged state through self-regulation under external disturbance. This study provides a theoretical basis for effectively dealing with the threat of external disturbance to the ecosystem. Based on the normalized difference vegetation index (NDVI) and meteorological factors data in the past 20 years, the net primary productivity (NPP) of vegetation was calculated using the Carnegie Ames Stanford Approach model. The mean value, ecosystem resistance, stability, and resilience for the NPP of vegetation in four periods (2001—2005, 2006—2010, 2011—2015, and 2016—2019) in the lower reaches of the Tarim River were studied and the ecosystem restoration status in different river sections and distinct periods was obtained. The ecosystem stability was reflected by analyzing the average NPP change, NPP range, variance, and coefficient of variation in the four periods. Smaller NPP range, variance, coefficient of variation, and FW slope in a certain period led to higher stability of the ecosystem. The ecosystem resistance was comprehensively reflected on the probability analysis of the NPP reduction based on frequency distribution and the prediction of minimum NPP based on the environmental index (EI). A larger NPP mean, stability, resistance, and maximum NPP are related to greater ecosystem resilience. The results revealed that: (1) in 2016—2019, the NPP exhibited the maximum mean and maximum value and the ecosystem recovery ability was larger compared with that of 2006—2015, but slightly smaller compared with that of 2001—2005. This behavior is probably related to the significant rise of groundwater depth and the increase of surface vegetation cover in the early stage of ecological water conveyance. (2) The resilience was the greatest for the upper section in 2011—2015 and middle and lower sections in 2016—2019. The lowest resilience for the upper, middle, and lower sections was observed in 2006—2010, which is probably related to the persistently low ecological water delivery in 2006—2010. (3) After 20 years of ecological water conveyance, the restoration of the ecosystem upper segment was better than that of the middle and lower segments. (4) The ecological restoration was related to a certain state, and the ecological resilience of the first 10 years after ecological water conveyance was relatively low, demonstrating the difficulty to restore the ecosystem to the non-degraded state, while the ecological resilience of the last 10 years was relatively high, indicating that the ecosystem is getting closer to the undegraded condition. Moreover, the overall vegetation growth is improving, suggesting that the area of receiving water in the desert riparian forest could be enlarged and the ecological benefit of water conveyance could be improved by branching the braided river in the future.