As a core component of the karst region in Southwest China, the Yunnan-Guizhou Plateau is characterized by extensive outcrops and widespread distribution of carbonate rocks. It functions not only as a critical ecological security barrier in Southwest China but also as a region with fragile ecosystems and concentrated ethnic minority communities. Plateau lake watersheds, as the most intensively exploited regions across the Yunnan-Guizhou Plateau, serves as ecological transition zones highly vulnerable to anthropogenic disturbances. The dynamic evolution of habitat quality in these basins directly impacts rivers' water conservation capacity, water resource allocation, and aquatic ecological security, while exerting far-reaching effects on local socio-economic development trajectories as well as agricultural production and construction. By integrating the In VEST model for habitat quality (HQ) assessment of karst lake watersheds with the Remote Sensing based Ecological Index (RSEI) model, this study aimed to enhance data reliability in habitat quality assessments of the Puzhehei watershed in Southeastern Yunnan. This approach enabled a comprehensive analysis of dynamic evolution patterns and future trends of habitat quality within the karst lake watershed. Key findings were as follows: (1) The RSEI value exhibited three temporal phases: initial decline, subsequent fluctuations, and a final upward trend. The basin-wide mean declined by 0.136 from 1990 to 2020, corresponding to an average annual decrease rate of 0.59%, primarily observed at ecological grade -1 and -2 (48.90%, 24.80%). (2) Temporal analysis of habitat quality revealed a trend of initial decline, followed by recovery, and subsequent decline. The basin-wide mean remained relatively stable from 1985 to 2020, fluctuating between 0.36 and 0.39, and consistently maintained ecological grade 2 (0.20 < HQ≤0.40), spanning 200.000-220.000 km² (60.00%-65.00%). (3) Incorporation of RSEI data demonstrated congruence between habitat quality and RSEI trends. Habitat quality declined by 0.132 from 1990 to 2020 (average annual decrease: 0.73%), manifested as a shift from ecological grade 3-4 (32.78%, 62.86%) in 1990 to grade 2-3 (16.61%, 81.65%) in 2020. Through systematic optimization, comparative analysis, and predictive modeling, the regional ecology of Puzhehei watershed in Southeastern Yunnan was shown to be in decline. Key differences were reflected in overall trends, extreme value distribution, mean value changes, and ecological grades. Model integration enhanced the scientific rigor of conclusions, providing a robust foundation for ecosystem protection in karst lake watersheds. Targeted conservation strategies were therefore essential for sustainable management of the Puzhehei watershed in Southeastern Yunnan.