The Crocodile Lizard (Shinisaurus crocodilurus) is the first-class protected wild animal. In recent years, crocodile lizards in the Beilou Station in Guangxi Daguishan Crocodile Lizard National Nature Reserve in China have been plagued by diseases, but the reasons are unknown. To investigate whether the occurrence of these diseases was related to the pollution of heavy metals and pesticides in food, this study detected heavy metals and pesticide residues in their main food using inductively coupled plasma mass spectrometry and chromatography mass spectrometry. Results showed that heavy metals were lower in the crocodile lizards compared with their food (earthworms), while pesticide residues were not detected in crocodile lizards and their food. These results indicate that it is less likely that heavy metals and pesticides accumulate in the crocodile lizards through biomagnification. Therefore, environmental pollutants such as heavy metals and pesticides have little effect on the occurrence of crocodile lizard disease. This study provides a references for the artificial rescue and breeding of crocodile lizards, which is benefit to the protection Crocodile Lizards.