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As a global biodiversity hotspot, southwestern China has been increasingly disturbed by human activities and has been undergoing rapid urbanization in recent years. In order to provide recommendations for conservation strategies, this paper explores the disequilibrium between land use and amphibian diversity. Four types of suitable habitat that are suitable for amphibians to inhabit (including farmland, woodland, grassland, and water habitat) were assessed and compared. Through fitting 20 models for species–area relationships (SARs), we found that different habitat types had different best-fitted SAR models. However, the conventional power law model had the advantage of being estimated without extreme values, and the estimation usually did not involve numerical problems. As such, we compared the debt mapping patterns derived from the best-fit SAR models and the power models. Regardless of the SAR models used, current amphibian richness was more strongly correlated with the past habitat area, suggesting that amphibian extinction debt existed in the region. Distribution of debt magnitude in different habitats presented congruent results: 1) The debt magnitude predicted in different habitats varied in decreasing order with grassland, water habitats, woodland, and farmland. 2) Debt magnitude in the region near the Chengdu Plain was high, while the extinction debt magnitude in the western region near the Qinghai-Tibet Plateau was low. This followed expectations, as there is a profound impact of human activities in the Chengdu Plain that threatens the survival of amphibian species in that area. In summary, our results suggest that some specific habitats (grasslands and water) and areas (Chengdu Plain) need greater conservation effort to better protect the habitats of amphibians and reduce the extinction risks of species.