Primary liver cancer is a leading cause of cancer-related death worldwide, and hepatocellular carcinoma (HCC) accounts for most cases. This study aimed to clarify the expression pattern, biological role, therapeutic relevance, and phosphoproteomic impact of farnesyl diphosphate synthase (FDPS) in HCC. FDPS expression was assessed in public datasets and clinical specimens using quantitative real-time polymerase chain reaction and immunohistochemistry. Its function was investigated through small interfering RNA-mediated silencing, lentiviral overexpression, pamidronate treatment, in vitro proliferation, migration, invasion, and apoptosis assays, xenograft models, phosphoproteomic profiling, and Western blot validation. FDPS was upregulated in HCC tissues and was potentially associated with poorer survival. FDPS silencing reduced HCC cell proliferation, migration, invasion, and tumorigenicity and increased apoptosis, whereas FDPS overexpression produced opposite effects. Pamidronate, a selective FDPS inhibitor, suppressed malignant phenotypes in vitro and inhibited tumor growth in vivo. Phosphoproteomic analysis revealed extensive phosphorylation changes after FDPS depletion, with enrichment in pathways related to GTPase and protein kinase C activation, glucose metabolism, cytoskeletal remodeling, immune regulation, cell cycle control, Golgi function, and ErbB and phospholipase D signaling. FDPS knockdown was further associated with decreased B-cell lymphoma 2 expression, reduced phosphorylation of Caspase-9 at Ser196, increased cleaved Caspase-3, and reduced phosphorylation of mechanistic target of rapamycin at Ser2448. Collectively, these findings suggest that FDPS contributes to HCC progression and may serve as a candidate biomarker and therapeutic target.