Multidrug resistance (MDR) in non-small cell lung cancer (NSCLC) causes chemotherapy failure, with lung cancer stem cells (LCSCs) playing a central role in the development of MDR. Although cathepsin L (CTSL) is known to be associated with tumor progression, its function in LCSCs and MDR remains unclear. The chemotherapeutic sensitivities of spheroid from NSCLC cell lines were evaluated using the CCK-8 assay. Western blot and qPCR analyses were performed to assess the expression levels of CTSL, stem cell markers (CD133 and CD44), stemness-maintaining molecules (OCT4 and SOX2), drug resistance proteins (MDR1 and ABCG2). In vivo experiments were conducted to validate the chemosensitizing effects of CTSL inhibitor, while the relationship between CTSL and the secretion levels of hepatocyte growth factor activator (HGFAC) and HGF was analyzed by RNA-seq, ELISA, qPCR and ChIP-qPCR methods. Our results demonstrated that spheroid cells exhibited pronounced MDR. High expression of CTSL correlated with poor prognosis in patients with NSCLC and enhanced MDR in NSCLC spheroids. Interfering with CTSL increased the sensitivity of NSCLC spheroids to multiple chemotherapy drugs while reducing cell stemness and survival. Moreover, the combination of CTSL inhibitor and docetaxel effectively suppressed tumor growth in vivo. Additionally, there is a positive correlation between CTSL and HGFAC at the mRNA level, and CTSL has a direct transcriptional regulatory effect on HGFAC. Finally, CTSL mediates chemotherapy resistance by regulating the expression of HGFAC/HGF/Met signaling pathway. Taken together, our findings establish CTSL as a pivotal driver of MDR in NSCLC, highlighting its promise as a therapeutic target to overcome this challenge.