Abstract: The responsibility of maintaining ecosystem circulation and biodiversity protection falls on key ecological function areas. It is of great significance to reveal the spatial-temporal evolution characteristics and influencing factors of habitat quality in key ecological functional areas to maintain regional ecological security and promote the harmonious development between man and nature. Based on ecosystem service value (ESV), habitat vitality and habitat threats, a habitat quality assessment model was introduced to analyze the habitat quality in ecological conservation area in Sichuan-Yunnan provinces from 2000 to 2018, while using the geographical detector model to quantify the impact of natural and social-economy factors. The results indicate that: (1) The overall level of habitat quality in the study area showed an upward trend, particularly in the southern part of the study area. The habitat quality grades were mainly at medium, higher or lower levels, while the trend of which was either from lower to medium or medium to higher. (2) 45.97% of the study area's habitat quality was at stable level, 43.46% showed an upward trend, and 10.57% showed an downward trend. Priority should be given to the latter to avoid further deterioration. (3) It turned out that natural factors such as altitude, temperature, topography and terrain, and the distance from waters, exerted primary influence on the spatial-temporal transfer process of habitat quality in the study area. In addition, impact of social-economy factors such as population density, GDP, distance from cities and towns, and night lighting is increasing. Compared with the effect either of natural factor or social-economy factor, the effect of interaction between natural and social-economy factors has profounder impact. This paper is concerned with illustrating the spatial-temporal evolution of habitat quality in ecological conservation area in Sichuan-Yunnan provinces, as well as providing reference for the construction and management of national key ecological function areas.