Objective To investigate the effects of hypoxia on the expression of E-cadherin, Vimentin, MMP-2 and MMP-9 in pancreatic cancer PANC-1 cells. Methods Pancreatic cancer PANC-1 cells were divided into control group and hypoxic group. The hypoxic conditions were 5% CO ₂, 2% O ₂ and 93% N ₂ while the control condition is 5% CO ₂ and 95% O ₂. The expression levels of E-cadherin, Vimentin, MMP-2 and MMP-9 were detected by qRT-PCR and Western blot. Results The E-cadherin protein expression of control group and hypoxia group were 0.859±0.087 and 0.321±0.033 respectively; the Vimentin protein were 0.453±0.051 and 1.128±0.169 respectively; E-cadherin mRNA were 1.125±0.092 and 0.352±0.036 respectively; Vimentin mRNA were1.253±0.130 and 2.875±0.366 respectively. All the differences were statistically significant (P<0.05); The MMP-2 protein and mRNA level in the control and hypoxia groups were 0.254±0.031 and 0.839±0.073, 1.230±0.125 and 4.369±0.368 respectively and the difference was statistically significant (P<0.05); The MMP-9 protein and mRNA in the control and hypoxia groups were 0.268±0.039and 0.733±0.075, 1.452±0.023and 4.136±0.569. The difference was statistically significant (P<0.05). Conclusion Hypoxia can promote the invasion and migration of pancreatic cancer cells by regulating the metastasis-related genes.