Dramatic land use change caused by human activities is one of the primary drivers of biodiversity loss. Clarifying the impacts of future land use change on biodiversity is of paramount importance for preserving biodiversity and maintaining human well-being. However, the previous studies have primarily focused on the impacts of future agricultural and urban expansion on biodiversity, while ignoring the comprehensive effects of other land-use changes, such as woodland, grassland and wet land on biodiversity. Based on the species richness data and future land use data under the coupled scenarios of different Shared Socioeconomic Pathways (SSPs) and Representative Concentration Pathways (RCPs), this study systematically assessed the changing trends of land use, species richness, and habitat quality in the Pearl River Delta region from 2015 to 2050 by integrating the Projecting Responses of Ecological Diversity in Changing Terrestrial Systems (PREDICTS) as well as the Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST) model. Then the study explored the combined impacts of future land use change on biodiversity by constructing a comprehensive biodiversity index. The results indicated that: (1) the primary type of future land use change under various scenarios in the Pearl River Delta region remained the expansion of built-up land, mainly encroaching on grasslands and concentrated in the central plain area. Conversely, land use changes in the hilly areas of the northeast and northwest primarily involved the conversion of cropland and grassland into woodland. These trends were mainly related to the setting of different SSP-RCP scenarios. (2) Species richness and habitat quality in the Pearl River Delta region exhibited a synergistic relationship and displayed similar spatial pattern changes. High-value areas and improvement areas mainly distributed in the northeastern, northwestern, and southwestern regions, which were characterized by abundant vegetation cover. In contrast, the central plain regions experienced degradation as the main trend due to the expansion of built-up land. (3) More than three-quarters of the Pearl River Delta region were projected to maintain relative stability in terms of the comprehensive biodiversity index. The other changing areas were characterized by slight or moderate declines, with fewer areas experiencing increases in the composite biodiversity index. This suggests that the overall ecological quality of the Pearl River Delta region may deteriorate in the future. The study can provide valuable references for the formulation of scientific ecological conservation and land use management policies in the Pearl River Delta region. This support aims to promote the sustainable development of the ecosystem and yield long-term benefits for socio-economic development.