Abstract Combination therapy using epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) and cytotoxic chemotherapy is a promising strategy to overcome resistance in non-small cell lung cancer (NSCLC). However, the complicated molecular mechanisms remain elusive. Here, we employed an integrated multi-omics approach to dissect the molecular responses to the third-generation EGFR-TKI Almonertinib (Alm) and paclitaxel (PTX) and their combination in EGFR-mutant NSCLC cells.