In the face of accelerating land use changes, conflicts between land use patterns and the eco-environment are increasingly pronounced. By calculating the eco-environment quality index (EQI) adopting the ecological–production–living spaces (EPLS) framework, we evaluate the eco-environment quality of land use changes within Chongqing’s central urban area from 2000 to 2020. The study employs a random forest model to elucidate the mechanisms influencing the eco-environment quality. The findings reveal the following: (1) Living spaces have expanded by 361.53 km2, while production and the ecological spaces have been experiencing a significant reduction of 331.42 km2 and 30.11 km2 over two decades. (2) The eco-environment quality has steadily declined from 0.3665 in 2000 to 0.3501 in 2020, indicating a degradation in overall quality. There is notable spatial variation in eco-environment quality, typically displaying a “low center–high periphery” pattern. (3) Pesticide usage, grain production, and the added value of the primary industry are the primary factors affecting ecological quality. The findings of this study provide valuable insights for global urban planning and environmental management. Rapidly, land use change regions worldwide face similar conflicts between economic growth and ecological sustainability. This research underscores the need for integrated land use policies that balance development with environmental preservation. The methodologies and findings can inform international efforts to optimize land use patterns, improve ecological quality, and achieving sustainable development goals, offering adaptable strategies for policymakers and urban planners globally.