Over the past 20 years, the implementation of a comprehensive plan for water resources of the Tarim River basin has resulted in ecological water delivery to Taitema Lake and Daxihaizi Reservoir of an average 350 million m³. However, two areas between the Wenkuer River and Old Tarim River, in the lower reaches of the Tarim River, have sparse vegetation and fragile ecological environments. Ecological restoration efforts over many years have not had a significant effect. In view of this, the study attempted to establish the medium-and long-term ecological optimization of the reservoir. A model was developed based on the Daxihaizi Reservoir as the main water body for regulation, the ecological water discharged from Daxihaizi, the ecological base flow in the river, the ecological water delivery of Taitema Lake, and the ecological water supply outside the river as ecological protection objects. The scheduling model was solved using particle swarm optimization. (1) Under optimal operation conditions, the Daxihaizi Reservoir had an average annual discharge volume of 523 million m³, which meets the 350 million m³ water requirement of the first phase of the Tarim River, and the downstream river channel had a significantly longer constant flow time. (2) With optimized discharge, the average volume of water entering Taitema Lake was 18 million m³, which is an increase of 20.0% compared with the measured data. The process for water entering the lake was more stable, which is conducive to consolidating the initially formed lake ecosystem. (3) With optimized discharge, the guaranteed rate of ecological base flow in the lower reaches of the Tarim River was 50.0%, and the guaranteed rate of continuous flow reached 64.6%. The improved ecological flows had an important positive effect on the ecosystem of the lower reaches of the Tarim River, which is greatly affected by human activities. (4) After the optimized operation, the average ecological water supply outside the lower reaches of the Tarim River was 167 million m³, laying a foundation for ecological restoration of the forests on the banks of the lower two rivers. These results have important application value for the restoration and protection of desert riparian vegetation in the lower reaches of the Tarim River. Such efforts could help to maintain the ecological health of river courses and tail lakes, and develop ecological groundwater banks.