Thioredoxin reductase (TrxR, TXNRD) is an essential enzyme implicated in the processes of cancer development and progression, positioning it as a promising target for cancer therapeutics. In this study, we employed target-based structural screening to identify berberrubine (BRB), a natural product characterized by an unprecedented isoquinoline scaffold that differs from known TrxR inhibitors. Our findings demonstrate that BRB serves as an effective inhibitor of TrxR, both in the context of the purified enzyme and within cancer cells. Since TrxR is highly expressed in non-small cell lung cancer (NSCLC) and is linked to patient prognosis and drug resistance, our results demonstrate, for the first time, that BRB can enhance the sensitivity of cisplatin to impede the proliferation of A549 cells, which was further confirmed in a xenograft model. The primary reason for cisplatin resistance in NSCLC is the DNA repair mechanism of apoptotic tumor cells. Our subsequent mechanistic investigation discovered that BRB selectively inhibits TrxR and impairs the biologically functional thioredoxin, which ultimately inhibits DNA synthesis and repair in cancer cells. Inhibition of TrxR by BRB led to a significant ROS accumulation in A549 cells, which contributed to oxidative stress-mediated apoptosis when used in combination with cisplatin. Our results conclude that BRB is a novel chemical entity of TrxR inhibitor that can increase the effectiveness of cisplatin in slowing down the growth of NSCLC both in vitro and in vivo. This provides a new perspective on the potential application of the combination of the two in the treatment of NSCLC.