To explore the impact of different transcription factor FOXM1 isoforms in breast cancer EMT process, the eukaryotic expression plasmids for two FOXM1 isoforms, FOXM1B-EGFP and FOXM1C-EGFP, were constructed and transfected into breast cancer cells. The expression levels of FOXM1 isoforms and EMT related genes in the cells were detected with RT-PCR and Western blot. The migration ability of the cells overexpressing the FOXM1 isoforms was measured with the transwell test. The FOXM1B-EGFP and FOXM1C-EGFP eukaryotic expression plasmids were successfully constructed. We found that the levels of exogenous FOXM1B in mesenchymal cells were higher than those in epithelial cells, and it was mainly located in the nucleus. The high levels of FOXM1B expression significantly stimulated the invasion of breast cancer cells and EMT process. The levels of exogenous FOXM1C in epithelial cells were higher than those in mesenchymal cells, and they were expressed in both the nucleus and the cytoplasm. The high levels of FOXM1C expression inhibited the invasion of breast cancer cells and EMT process. FOXM1B was located mainly in the nucleus of cells and FOXM1C was expressed in both the nucleus and the cytoplasm of cells. The research has indicated that FOXM1B and FOXM1C play different roles in the process of EMT of breast cancer cells.