The Three Gorges Project, a world-class water conservancy project, was built in 2020 and set a new world record in annual electricity generation. It is undeniable that it has brought considerable ecological benefits together with economic and social benefits to the Three Gorges Reservoir Area (TGRA). It is full of practical significance to evaluate the green development performance level (GDPL) in the TGRA, which is a new indicator reflecting the comprehensive performance of the Three Gorges Project. This study focuses on evaluating the GDPL in the TGRA. First, we established a novel evaluation system for GDPL in the TGRA, and then the GDPL of 26 regions in the TGRA from 2000 to 2020 were calculated by using overall entropy method and expert scoring method to analyze the development performance of environmental system, economic system and social system and their coupling coordination degree. Also, the temporal and spatial evolution process, regional disparity, and spatial correlation of GDPL in the TGRA were examined through exploratory spatial data analysis (ESDA). The results show that: (1) the GDPL in the TGRA is in a medium level with a score of 0.3–0.4 and is growing stably. Ecological protection and development quality contribute greatly to the GDPL and the inter-regional differences between the head, the belly and the tail sections are narrowing. (2) The coupling degree between the environmental system, economic system and social system in the TGRA is as high as above 0.8, but the coupling coordination degree is only about 0.3. (3) The GDPL in TGRA varies with the region and is at a high level in the belly section, a medium level in the head and tail sections. The six regions in the belly section and one in the tail section, which are of a high level of GDPL, form a shape of the Big Dipper. (4) The global spatial correlation was not obvious in most years except the year of 2000, 2017, 2018 and 2019. The Lisa cluster map shows clusters only emerge in the head and the tail sections, the belly section, in which the GDPL is high, doesn’t show spatial agglomeration. These findings can not only provide references for promoting green development in the TGRA, but also enrich the study of the evaluation of GDPL.