Abstract: Understanding the spatial and temporal differentiation of ecological quality in the context of agricultural land consolidation is essential for effective planning and decision-making. In this study, the spatial and temporal differentiation patterns and dynamic processes of ecological quality within the project area (267 agricultural land consolidation projects in the Qijiang District of Chongqing City) were investigated from 2000 to 2020 using a Remote Sensing-based Ecological Index (RSEI) model. A comparative analysis was conducted to assess the ecological quality characteristics of the project area in relation to varying frequencies of consolidation, thereby elucidating the factors contributing to the observed disparities in ecological quality across the agricultural land consolidation project sites. The results show that: 1) Over the past two decades, the ecological quality in the agricultural land consolidation project area of Qijiang District has been generally good, with the RSEI showing a "V" shaped trend, first declining and then rising, resulting in an overall improvement. Long-term agricultural land consolidation has a significant positive impact on regional ecological quality. During Phase 1 (2000–2010), some disturbance to the regional ecological environment was observed, whereas in Phase 2 (2011–2015) and Phase 3 (2016–2020) ecological quality was promoted. From the perspective of project implementation, ecological quality showed a continuous optimization trend at 5, 10, and 15 a post-implementation, highlighting the lasting and profound impact of agricultural land consolidation projects on regional ecological restoration and optimization. 2) Between 2000 and 2020, 267 project areas demonstrated favorable ecological quality, comprising > 55% of the overall project zone area. By contrast, regions classified as poor or very poor constituted less than 3% of the total area. Analysis of the various consolidation phases revealed that the initial phase of the project resulted in a notable decline in areas characterized by high and good ecological quality. Conversely, the second and third phases contributed to the enhancement of the regional ecological environment by optimizing areas of medium and good quality. 3) The frequency of agricultural land consolidation initiatives was positively correlated with the ecological quality of the respective project area. This indicates that an increase in consolidation efforts within the same region is associated with a more pronounced enhancement in ecological quality. 4) Changes in the ecological quality of the agricultural land consolidation project area result from the combined effects of natural and socioeconomic factors. The first phase of the project was mainly driven by the scale of construction and the increase in arable land area, whereas the second and third phases were primarily influenced by the interaction between project type and altitude. The research outcomes enhance our understanding of alterations in ecological quality within areas designated for agricultural land consolidation projects. These findings serve as valuable references for agricultural land consolidation and ecological monitoring in hilly and mountainous regions.