Taxus chinensis var. mairei (TC) is a traditional Chinese ornamental and medicinal plant, the leaves and twigs of which are used in anti-tumor therapy in southern China. However, the mechanism and role of aqueous extract of TC (AETC) in promoting apoptosis in non-small cell lung cancer (NSCLC) cell lines has remained unclear. In this research, we observed that AETC inhibited the suppression of the proliferation of NSCLC cells and highly inhibited the proliferation of NCI-1975 cells. Furthermore, AETC exerted minimal inhibitory effects on normal human lung epithelial cells and induced apoptosis in NCI-1975 and A549 cells. The findings of RNA sequencing, qRT-PCR, western blotting, and immunofluorescence showed that upregulated ATF3 expression and ATF3 gene knockdown, respectively, increased and decreased the anti-tumor effects of AETC associated with Hippo pathway inhibition and decreased YAP degradation. Furthermore, AETC reduced the tumor volume and weight in nude mice; upregulated ATF3, p-MOB1, and p-YAP (Ser397); and actively regulated cleaved PARP and cleaved caspase-9/8/3. These findings suggest that AETC induced NSCLC cell apoptosis via the ATF3-Hippo-YAP pathway in vivo and in vitro. We also found that AETC is non-toxic to normal cells and nude mice. Thus, AETC might represent a promising adjuvant for anti-tumor therapy against NSCLC.