Land use activities play an essential role in habitat degradation and restoration. As priority zones for global habitat conservation, studying the impact of land use activities on habitat quality (HQ) in the World Protected Areas (WDPA) has great importance. However, insights into land use activities and HQ in the WDPA remain scarce and their relationship is still unclear. Here, we assessed land use activities and HQ in the WDPA over the past 20 years and analyzed the impact of land use activities on HQ. The results showed that forestland was the dominant land use type in the WDPA and that the area of forestland, bare land, and water area decreased while the area of other land use types increased during the study period. Land use change in protected areas in different continents shows great differences. Land use intensity (LUI) in the WDPA increased over the 20 years, but HQ remained largely unchanged. LUI increased but HQ decreased was the main change type of grid cells in the WDPA. The bivariate spatial autocorrelation results showed that High-Low (high HQ and low LUI) clusters were the dominant clustering type in the WDPA, while Low-High (low HQ and high LUI) clusters were the least represented clustering type. The regression results showed that LUI tended to have a negative effect on HQ in forested areas and a positive effect on HQ in desert, permafrost areas. These findings can provide a reference for effective land use differentiation control measures and biodiversity conservation measures in the WDPA.