Objective To investigate the effect of Siwuyin on the migration and invasion of esophageal cancer cells and explore the molecular mechanisms of this effect. Methods Different concentrations (600 μg / mL, 300 μg / mL, 150 μg / mL, 70 μg / mL, and 30 μg / mL) of Siwuyin were applied to the human esophageal cancer cell line Eca109. The blank control group did not undergo any treatment. IncuCyte software was used to evaluate the scratch closure rate and to screen the effective concentration and intervention time of Siwuyin. The effect of Siwuyin on cell invasion was observed using a transwell system, while laser confocal microscopy was used to observe the effect of Siwuyin on the cytoskeleton of microfilaments. In addition, RNA-Seq sequencing and information analyses were used to determine the effect of Siwuyin on RNA in esophageal cancer cells. Results The scratch assay result demonstrated that when the concentration of Siwuyin was 150 μg / mL, cell migration ability was significantly inhibited ( P < 0. 05). Results from the transwell experiments revealed that Siwuyin significantly inhibited the invasion of esophageal cancer cells ( P< 0. 05). Furthermore, laser confocal microscopy demonstrated that Siwuyin significantly inhibited the epithelial-mesenchymal transition of esophageal cancer cells. Finally, RNA-Seq analysis revealed that Siwuyin altered the metabolic pathways of alanine, aspartic acid, and glutamate in esophageal cancer cells, and this effect mainly inhibited the production of fumaric acid. Conclusions Siwuyin can significantly inhibit the migration and invasion of esophageal cancer cells and inhibits the accumulation of fumarate.