Autophagy is one of the most common protective mechanisms during plant stress response. We studied the effect of exogenous Cd on autophagy in celery, by using transcriptome sequencing technique to analyze the differentially expressed genes under different Cd concentrations (0, 2, 4 and 8 mg/L). Eight differentially expressed autophagy-related genes were screened and identified by qRT-PCR. Cd had obvious toxic effect on celery, in a dose-dependent manner. Eight differentially expressed autophagy-related genes were screened, among which ATG8a, ATG8f, ATG13, AMPK-1 and AMPK-2 were up-regulated, whereas ATG12, VPS30 and VPS34 were first up-regulated and then decreased. The up-regulated expression of differential genes may resist Cd toxicity by increasing autophagosome structures; however, 8 mg/L Cd exceeded the autophagosome tolerance limit of celery, resulting in decreased expression of multiple autophagy-related genes. The above results can provide help for subsequent functional study of autophagy-related genes, and provide a reference for further exploring the tolerance mechanism of celery to Cd toxicity.