Background Non-small cell lung cancer (NSCLC) is one of the leading causes of cancer-related death around the world. Epithelial–mesenchymal transition (EMT) has been documented to increase motility and invasiveness of cancer cells, which promotes cancer metastases. Purpose This study aims to investigate the inhibitory effects and mechanisms of the dinorditerpenoids and norditerpenoids isolated from the seeds of Podocarpus nagi against transforming growth factor (TGF)-β1-induced EMT. Methods A series of dinorditerpenoids and norditerpenoids were isolated from the seeds of P. nagi. Western blot and quantitative real-time PCR assays were performed to determine the expression levels of relative proteins and mRNA, along with immunofluorescence, SBE-luciferase and ChIP assays for the mechanism study. Transwell assays were conducted to determine the effect of the compounds on cell migration and invasion. Results Nagilactone E (NLE) showed the superior inhibitory effect against TGF-β1-induced EMT. NLE treatment dramatically inhibited TGF-β1-induced expression of EMT markers in A549 cells. Mechanism study indicated that NLE markedly suppressed TGF-β1-induced Smad2 and Smad3 activation and nuclear translocation. NLE treatment attenuated the protein and mRNA levels of TGF-β receptor TβRI. SBE-luciferase and ChIP assays showed that NLE inhibited the combining of Smad3 to SBE in the promoters of the cell signaling factors. NLE inhibited TGF-β1-stimulated cell migration and invasion. NLE co-treatment inhibited TGF-β1-induced up-regulation of the key signaling proteins related with migration and invasion. Conclusion NLE inhibited TGF-β/Smad signaling pathway, thereafter suppressed TGF-β1-induced EMT, migration and invasion in NSCLC A549 cells.