Effectively evaluating the effects of future urban expansion on natural habitat quality (NHQ) is critical for improving the sustainability of regional and even global cities. However, because of the difficulties in simulating spatiotemporal distribution of future urban expansion and the uncertainties in future socioeconomic development, effectively evaluating the effects of future urban expansion on NHQ is still challenging. Using the Hohhot-Baotou-Ordos-Yulin (HBOY) urban agglomeration in China as an example, this study simulated future urban expansion and evaluated its effects on NHQ. We first quantified the NHQ spatial patterns in HBOY using the Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST) model. Second, we simulated urban expansion in HBOY from 2017 to 2050 by coupling localized Shared Socioeconomic Pathways (SSPs) and the Land Use Scenario Dynamics-urban (LUSD-urban) model. Finally, we evaluated the effects of future urban expansion on NHQ by calculating the degradation rate of NHQ in the entire region and in different types of cities. We found that coupling localized SSPs and the LUSD-urban model can effectively evaluate the effects of future urban expansion on NHQ. Compared with coupling original SSPs and the LUSD-urban model, in HBOY case study, our method reduced the absolute of the evaluation error from 5.17 to 11.43% to 2.86–5.17%. The results showed that under all localized SSPs, the urban expansion from 2017 to 2050 in large cities will lead to the most obvious decrease in regional NHQ of 4.85–7.32%, while that in medium cities and small cities will be 1.23–2.37% and 0.19–0.35%, respectively. Therefore, we suggest that SSPs should be localized when used to simulate the effects of future urban expansion on NHQ. In addition, in order to achieve the sustainable development goals, the HBOY urban agglomeration should control the urban size and optimize the urban spatial pattern, especially for large cities, in the future to reduce the impacts of urban expansion on NHQ.