Habitat quality is an important indicator for evaluating the biodiversity provided by ecosystem. Estimating and scenario-simulating the dynamic evolution and future development trends of habitat quality under the influence of land-use change is significant in regional biodiversity conservation, formulating land-use planning, and maintaining the ecological environmental sustainability. In this article, we included the Huaihe River Economic Belt as the area of study because of its vital location in China and applied the CA-Markov and InVEST models to analyze the spatio-temporal evolution of habitat quality and to simulate the future development trends of habitat quality under three different land-use scenarios: fast urban growth scenario, farmland conservation-oriented scenario, and ecological conservation-oriented scenario. The results showed that the land-use change in the Huaihe River Economic Belt was mostly represented by the continuous increase of the built-up area, whereas other land types all declined in area from 1995 to 2015. The land-use changes under these three abovementioned alternative future scenarios with different development orientations were considerably different. The built-up area has been shown to expand rapidly to occupy other land types on a large scale under the fast urban growth scenario. Urban land increased slightly and a large area of rural residential land would be converted into farmland under the farmland conservation-oriented scenario. The built-up area and farmland might decrease while woodland, grassland and water would increase in extent of areas under the ecological conservation-oriented scenario. Habitat quality has been shown to be generally poor, continuing to decline from 1995 to 2015, while its spatial distribution was higher in the southwest and northeast areas and lower in the central regions. The future habitat quality would display a downward trend under the fast urban growth and farmland conservation-oriented scenarios with a further deterioration of the ecological environment, while the ecological conservation-oriented scenario predicted the converse trend that the ecological environment would be improved productively. This study may be useful for understanding the impact of land-use dynamics on biodiversity. The research results can provide a scientific basis for the decision-makers to formulate biodiversity conservation and land management policies.