Pancreatic cancer is one of the most common malignant tumors of the digestive system, with the majority of patients not succumbing to the primary tumor but rather to metastasis. Epithelial-mesenchymal transition (EMT) is abnormally activated in numerous cancers, whereby it promotes tumor cell migration and invasion. Yes-associated protein 1 (YAP1) is commonly overexpressed in various cancer types and plays an oncogenic role. We demonstrated that FV-429, a derivative of the natural flavonoid wogonin, inhibited the invasion and metastasis of pancreatic cancer cells by modulating EMT-related proteins. FV-429 enhances the expression of p-LATS1, thereby promoting the conversion of YAP1 to p-YAP1. Meanwhile, it suppresses the nuclear translocation of YAP1, thereby affecting the expression of E-cadherin and snail1, which, in turn, impacts the EMT. The Hippo-signaling pathway inhibitor TDI-011536 was used to validate these results. In vivo, a mouse model of pancreatic cancer lung metastasis was established using PANC02 cells to validate the antimetastatic effect of FV-429, which confirmed its action through the Hippo/YAP1 pathway. In addition, FV-429 demonstrated high safety and low toxicity. In conclusion, we demonstrated that FV-429 inhibits migration, invasion, and metastasis of human pancreatic cancer cells by affecting the Hippo/YAP1 pathway, suggesting that FV-429 has the potential to be a novel therapeutic agent for pancreatic cancer.