Objective To study the regulation of Wnt pathway in the mouse embryonic stem cells after sustained exposure to Wnt3a. Methods The ES-E14TG2a mouse stem cells were cultured with the exogenous Wnt3a(100ng/ml) for 21 days, the expression of β-catenin was detected by immunofluorescence and western blotting assay. RT-PCR analysis was performed to assess the expression of Wnt pathway downstream genes. F text and LSD were used to compare the difference between the groups. Results Activation of the Wnt pathway led to accumulation of dephosphorylated catenin in the cytoplasm after 21 days. The expression of Wnt downstream target genes such as Pitx2, Frizzled, Sox17 and Oct4 tended to increase at the same time. The mean values of Pitx2, Frizzled and Sox17 on days 7, 14 and 21 were 4.17 ± 0.20, 7.27 ± 0.35 174and 8.59 ± 0.21(F = 222.757,P = 0.000); 1.01 ± 0.06, 2.93 ± 0.22 and 5.44 ± 0.30(F = 302.703,P = 0.000); 8.45 ± 0.41, 18.35 ± 0.17 and 34.93 ± 0.16(F = 7217.083,P = 0.000). respectively. Conclusion Wnt pathway can be activated by exogenous Wnt3a in mouse embryonic stem cells, which can further upregulate Wnt downstream genes.