Clarifying the spatial and temporal evolution characteristics of the ecological environment quality of World Heritage Karst Sites (WHKSs) and its response to different rocky desertification grades at spatial scales is crucial for the monitoring and protection of WHKSs as well as the implementation of ecological and environmental policies in karst regions. The ecological evaluation model of Remote Sensing Ecological Index (RSEI) was used to evaluate the ecological environment of Libo–Huanjiang World Heritage Karst site and Shibing World Heritage Karst site, and then the spatial autocorrelation and geo-detection model was used to further analyze the ecological environment, and final spatial overlay of RSEI and rocky desertification by year to analyze the linkage relationship between RSEI and rocky desertification. The results showed that (1) in the three-phase ecological environmental quality evaluation of the two heritage sites, the RSEI in 2010, 2016, and 2022 reached 0.60, 0.67, and 0.64 for the Libo–Huanjiang heritage site, and RSEI in 2010, 2016, and 2022 for the Shibing heritage site reached 0.60, 0.74, and 0.70, respectively; (2) the RSEI of both heritage sites show a gradually increasing positive spatial correlation, and has significant spatial aggregation characteristics, with both heritage sites dominated by the high-high and low-low spatial aggregation categories; (3) both heritage sites have the highest degree of explanation of changes in ecological quality by the NDBSI factor, indicating that this factor plays a key role in changes in ecological quality at heritage sites; (4) the response of the RSEI mean value of Libo–Huanjiang in each grade of rocky desertification area is, from high to low, no rocky desertification, non-karst, potential rocky desertification, mild rocky desertification, moderate rocky desertification, intensive rocky desertification, and extreme intensity rocky desertification, and the response of the RSEI mean value of Shibing is, from high to low, non-karst, no rocky desertification, potential rocky desertification, mild rocky desertification, and moderate rocky desertification. The spatial superposition analysis of the RSEI index and rocky desertification index can quantitatively study the changing status of the ecological environment in different rocky desertification areas, and the results of the study can provide theoretical references for the environmental monitoring and the prevention and control of rocky desertification in the karst areas and WHKSs.