Hengduan Mountainous Region (HMR) is one of the top 25th biodiversity hotspots in the world, and its ecological security and biodiversity conservation have increasingly attracted much attention from China and other countries. Economic and social development has brought many new challenges to the survival of Diploderma, the endemic species of the HMR. The original habitats of several Diploderma species have completely been destroyed because of road construction and hydropower projects, and what made us worrying was some species that have become extinct in local areas. Therefore, timely research on the conservation ecology of Diploderma is very important and urgent to the design of conservation plan. Habitat preference and morphological differentiation are important contents of conservation ecology research. In this study, the habitat factors including habitat type, vegetation coverage, vegetation height, stone size, distance road, interference factor, slope direction, slope position, gradient, temperature, and humidity of 9 Diploderma species in HMR were measured by line and square to transect. At the same time, the morphological characters of 19 Diploderma species were quantified using field sampling and herbarium specimen. Habitat preference and morphological differentiation were analyzed using Generalized Linear Mixed Model (GLMM) and Phylogenetic Generalized least-squares (PGLS). The results showed that Diploderma from different habitat types had special preferences for habitat factors. The species distributed in shrub preferred the habitats with stone, brush, steeper sunny slopes, large stone size, and suitable temperature (25-35℃), with Incarvillea arguta. The species distributed in forest preferred the habitats with big trees, steeper hill and high vegetation coverage, with Bauhinia×blakeana. Our results also showed much differentiation in body size and locomotion characters between shrub-type and forest-type lizard. For males, forest distributing species possessed large size in tail length, nose-eye distance, 4th finger length and claw length of the 4th toe compared with shrub distribution species, meanwhile snout length and shin length were just the opposite. While for females, forest distribution species possessed large size in tail length, head length, snout length, nose-eye distance, 4th finger length, 4th toe length and claw length of the 4th toe compared with shrub distribution species. Taken together, our study provides direct evidence for habitat preference and morphological differentiation of the endemic lizards' species in HMR, while it would greatly contribute to the understanding of adaptation tactics towards the dry-hot valley habitat in Diploderma, as well as provide important support for the design of conservation plan.