Ecological zoning planning is an important means to balance regionally ecological protection and development, and to promote regional sustainable development. Taking Bortala Mongolian Autonomous Prefecture as an example, the ecological zoning planning was carried out on the basis of assessing the habitat quality and human footprint index in the study area by coupling the InVEST-HFI-PLUS model. Based on the land use data of 2005 and 2020, the PLUS model was used to simulate the land use status in 2035 under the two scenarios with natural development and planned protection, to evaluate the ecosystem service level under different scenarios, and to compare and analyze the actual benefits of different scenarios. The results indicated that:(1) the overall habitat quality of the study area was good, and 56% of the regions had high habitat quality grade. The HFI(Human footprint index) showed a pattern of low in the periphery and high in the middle of the study area. (2) Based on the combination of habitat quality and human footprint index, the study area could be divided into three ecological control zones:key protection area, key restoration area, and moderate development area. The key protection area accounted for 52.8%, the key restoration area accounted for 42%, and the moderate development area accounted for 5.2%. (3) Based on the land use simulation and ecosystem service value assessment in 2035 under the two scenarios, the total value of ecosystem services under the planned conservation scenario would be 416 million yuan higher than that under the natural development scenario, and the ecological conditions in the study area would be significantly improved.