Hepatocellular carcinoma (HCC) is a malignant tumor associated with high global incidence and mortality rates. Proteomics, as a platform technology of cellular protein expression, modification, and interaction, has provided innovative perspectives on early diagnosis, treatment, and targeted drug development for HCC. This review summarizes recent progress in proteomics for advancing HCC biomarker discovery, drug target identification, and understanding drug action mechanisms. Proteomic technologies, including mass spectrometry for specific protein signatures identification, protein microarrays for high-throughput analysis, and bioinformatics for data interpretation, have profoundly promoted the identification of liver cancer-specific biomarkers. These advancements not only facilitate early diagnosis but also improve prognostic assessment. Proteomics is pivotal in expediting the discovery and development of new drugs, providing more effective and personalized treatment options for HCC patients. This review offers a comprehensive overview of the applications of proteomics in anti-HCC drug research, serving as a reference to further advance the development of HCC research and treatment domains.