Changes of land use caused by urbanization and human activities have seriously affected quality habitat of urban green space, resulting in a series of environmental crises. How to strategically coordinate the relationship between land use construction and green space habitat quality is an important part of urban sustainable development. Although many scholars have explored the impact of many factors on natural habitats, from intense expansion of land construction, landscape pattern change, to land use type change and more, there is still little research on how land use scale, shape, intensity and other aspects affect habitat quality from the perspective of compact land use. Take the three construction periods in Wuhan (2005, 2013 and 2018) for an example. This paper firstly constructs a comprehensive evaluation system of habitat quality from the perspective of habitat aptness and carrying capacity, and a land use compactness evaluation system is built based on land use intensity and land function layout. Secondly, the paper divides the study sample into cold spot area, hot spot area and habitat change area according to the hot spot distribution of habitat quality in the three periods. Finally, through correlation and spatial autocorrelation analysis, the paper explores the relationship between habitat quality and land use compactness in addition to its spatial correlation pattern. The results show that:(1) The compact change of land use in Wuhan has a negative impact on local habitat quality. From 2005 to 2018, the habitat quality decreased from 0.624 to 0.578, and its spatial and temporal differentiation characteristics were obvious, showing a low quality in center area and high quality in periphery across the three periods. The overall degradation of habitat quality is accelerated, and the improvement of urban habitat quality is not significant. The urban development boundary is the key area of habitat quality degradation; (2) The degree to which the habitat quality is affected by the compactness of land use in different areas shows obvious differences. The cold spot area of habitat is most significantly affected by the compactness of land use. The affect in habitat change area has strong correlations with the density of construction land, residential land, road network, land aggregation, diversity of land use, and density of bus stops; (3) The compactness of land use, as a factor, will have a potential impact on the habitat quality of the surrounding area. The five indicators of construction land density, land aggregation, land use diversity, land mix, and road network density not only affect the habitat quality of the land parcel, but also have a close relationship with the degradation of the habitat quality of the surrounding land parcel. They have a wide range of impacts on the habitat, and the integration of land use has a small impact on the habitat quality. The research results have significant references for optimizing land use pattern, maintaining high quality of habitat, realizing efficient land allocation and improving green space ecosystem.