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As an important ecological barrier in the Guangdong-Hong Kong-Macao Greater Bay Area, Shimentai Nature Reserve aims to protect the integrity of the ecosystem and biodiversity. It was established as a provincial-level nature reserve in 1998 and upgraded to a national level nature reserve in 2012. However, the changes in the quality of the ecological environment remain unclear. This study quantitatively assessed the changes in the ecological quality of the Shimentai Nature Reserve from 1997 to 2021 based on the Remote Sensing Ecological Index (RSEI), explored the changes in ecological quality before and after the establishment of the nature reserve and the upgrading of the control level, and discussed the reasons for the evolution using the Random Forest Algorithm and correlation analysis method. The results showed that the RSEI value of Shimentai Nature Reserve dynamically increased from 0.637 in 1997 to 0.714 in 2011, and the ecological environment quality steadily improved as the nature reserve was upgraded from the provincial to the national level; the RSEI reached 0.788 by 2021. The quality of the ecological environment has improved in 64.5% of the protected area, the buffer zone has improved more obviously, and the deteriorated areas are mainly concentrated in the experimental area where human activities are frequent and in the high-altitude ridge area in the core area. Meanwhile, the ecological environment quality of the buffer zone and the low-altitude area in the core area is adequate and relatively stable. The RSEI responded most clearly to elevation, with the best ecological quality between 300 and 600 m and relatively poorer quality above 900 m. On the slope upward with the south slope as the turning point, the quality of the ecological environment gradually improved from the north slope to the south slope in a clockwise direction, and then gradually deteriorated from the south slope to the north slope. At a cut-off point of 15° on the slope, the RSEI briefly increased and then decreased continuously. The RSEI was highest at a soil pH of 5.3, organic carbon mass fraction of 4.1%, and clay mass fraction of 32%. The degree of influence of residential activities on the quality of the ecological environment from the outside to the inside (i.e., the experimental area-buffer area-core area) was gradually reduced and negatively affected. The RSEI was positively correlated with precipitation, 23.6% of the area passed the significance test (P < 0.05). The local year was influenced by precipitation, and the influence of precipitation was greater in certain years. Overall, the ecological environment quality of the Shimentai Nature Reserve has shown a clear improvement trend, and the protection and management of the bare soil areas on the top of the high mountains, and the areas of frequent human activities in the lower altitudes, should be strengthened in the future.