Abstract: The Songhua River Basin plays a pivotal role in regional water supply, biodiversity conservation, ecosystem stability, socioeconomic development, and natural disaster prevention and control. However, with the acceleration of urbanization, a series of ecological and environmental quality issues have emerged in the basin. Against this backdrop, this study examined the spatiotemporal dynamics of habitat quality and land use/land cover (LULC) in the Songhua River Basin over the past three decades, and explored their intricate relationships: aiming to provide actionable insights for ecological protection and management in the region. Using LULC data from 1990 to 2020, we employed the InVEST model, land use transfer matrix, and spatial autocorrelation model to analyze the characteristics of habitat quality and LULC changes, as well as to clarify the response relationship between these two factors. The main results were as follows: from 1990 to 2020, the overall habitat quality of the Songhua River Basin showed a downward trend. The proportion of grids with medium habitat quality increased by 25.70%, while that of grids with high and very high habitat quality decreased by 5.17%. Habitat degradation was primarily concentrated in the central urban agglomerations and the ecologically fragile western regions of the basin. Notable changes in LULC were observed over the study period: both the extent and spatial configuration of cultivated land, construction land, and water bodies changed markedly. Land use conversions that exerted positive impacts on habitat quality included the shift from cultivated land to forest land (contribution ratio: 0.466) and from unused land to grassland (contribution ratio: 0.302). In contrast, conversions with significant negative impacts were: forest land to cultivated land (contribution ratio: −1.013), grassland to cultivated land (contribution ratio: −0.852), cultivated land to construction land (contribution ratio: −0.405), and water bodies to unused land (contribution ratio: −0.461). In terms of spatial distribution, habitat quality was relatively low in the central basin, yet significantly higher in the southeastern and northern regions. The global spatial autocorrelation Moran’s I values for habitat quality ranged from 0.849 094 to 0.852 893, indicating a pronounced spatial agglomeration pattern with clustering intensity on the rise over the decades. Areas with high habitat quality were mainly distributed in the upper and lower reaches of the basin, while low-quality areas were concentrated in the middle reaches. These results offer a scientific foundation for developing integrated strategies that balance regional ecological improvement with economic growth, enhance the protection and management of inland river systems, and optimize the complex plain-grassland-forest-river ecosystem pattern within the basin.