The Hehuang Valley is located in the transitional region between the Qinghai-Tibet Plateau and the Loess Plateau, and is the economic and cultural center of Qinghai Province. The fragile ecological environment in this region is in conflict with the intense human activities. For the assessment of habitat quality in ecologically sensitive areas under landscape pattern change, this study highlighted the transformation process among different landscape types by using the improved flow transfer matrix, and calculated the habitat quality of the Hehuang Valley from 1995 to 2015 with the Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) model, analyzing its spatiotemporal change and cold-hot spot distribution characteristics, along with characterizing the correlation between habitat quality and landscape pattern elements with gray relational degree. The results show that: (1) From 1995 to 2015, grassland, construction land, and water area kept increasing, and landscape types showed the characteristics of fragmentation, complexity, and heterogeneity. (2) Habitat quality of the Hehuang Valley was divided by the line connecting Guide County and Ledu County higher habitat quality and more concentrated hotspots were distributed to the south of this line. (3) Correlation between habitat quality and landscape pattern indices including Shannon’s Diversity Index (SHDI), Shannon’s Evenness Index (SHEI), Landscape Division Index (DIVISION), Contagion (CONTAG), Largest Patch Index (LPI) and the scale of forest land and grassland is higher, and is lower with construction land area, showing that under the influence of ecological protection policies, construction land increased by occupying landscape types other than high quality habitat types, such as forest land and grassland. The results can be used to guide the identification of ecologically sensitive areas and the demarcation of ecological red line in the Hehuang Valley.