In this study, an EIORES-DEA high-quality development indicator system based on efficiency was constructed by selecting multiple indicators from six aspects: economic development, innovation vitality, openness to the outside world, resource utilization, ecological security, and social progress. The weights of the indicators were determined via the entropy weighting method, and the high-quality development (HQD) efficiency of 38 districts and counties in Chongqing municipality from 2010 to 2021 was measured by the Super epsilon-based measure (EBM) model. The spatial and temporal evolutions of efficiency were visualized by combining GIS technology, and the spatial pattern of the HQD level was determined using the LISA time path. The spatial aggregation characteristics of efficiency were revealed utilizing Moran’s I index and spatial trend surface analysis. The results showed that the HQD level in Chongqing rose in an N-shaped fluctuation, and the HQD level in the central city was much higher than that in the new main city, southeast Chongqing, and northeast Chongqing. The high-efficiency (H-efficiency) regions were not connected together but rather distributed independently, with most of the medium–high-efficiency districts and counties distributed around the H-efficiency districts and counties. Meanwhile, the H–H agglomeration area had frequent turnovers in different years, indicating that the competition between H-efficiency districts and counties is intense and that the development synergy among them is poor, while the L–L agglomeration area fluctuated greatly in a given year but gradually stabilized in recent years. The spatial trajectory of HQD in Chongqing municipality mainly moved back and forth along the southwest–northeast direction, which is consistent with the direction of the Yangtze River. Finally, the imbalance of HQD development in Chongqing municipality mainly stems from the regional east–west development differences.