Thirty-six habitat characteristics of Chinese crocodile lizards (Shinisaurus crocodilurus) were studied from July to August 2005 in the Luokeng Nature Reserve in Guangdong Province. In the distribution area of Chinese crocodile lizards in the Nature Reserve, we selected 30 streams by chance and used the line transect method to survey the animals and measured 15 ecological factors of the habitats of the animals. Results from Principle Components Analysis showed that nine ecological factors affected the habitat preference of Chinese crocodile lizards significantly. These included: the width, and length of the backwater pool, the distance to water bodies, the water velocity, perch height, perch diameter, the distance to human disturbance, vegetation coverage, and vegetation type. The influence of the composition of the pool bottom, the water depth, living and dry condition of the perch, perch slope, stream type and slope aspect were not significant. The habitat preference of Chinese crocodile lizards is: middle width (1-2 m) and length (1-2 m) of backwater pool, above the water body, slow water velocity, middle perch height (0.5-1.0 m), small perch diameter (≤1.00 cm), far away from human disturbance (distance>500 m), broadleaf forest and coverage >60%. It is necessary to improve the awareness of residents, protect water and conserve forest and vegetation on both sides of streams.