Background and Aims: Hepatocellular carcinoma (HCC) is a highly heterogeneous cancer, with mechanisms of initiation, progression, and recurrence not fully clarified. While prior large-scale phosphoproteomic studies in HCC have mapped phosphorylation dynamics and identified subgroups consistent with proteomic subgroups, the role of phosphorylation in early-stage HCC heterogeneity and therapeutic vulnerabilities remains unexplored. Here, we aimed to provide a phosphoproteomic characterization in early-stage HCC, elucidate dysregulated signaling pathways and kinases, investigate the heterogeneity of HCC, and identify treatment vulnerabilities. Approach and Results: By interrogating the phosphoproteome and proteome in HCC, unlike previous studies on mRNA and protein levels, we identified a marked reduction in phosphorylation regulation of EGFR-mediated canonical ERK/MAPK signaling, accompanied by elevation of atypical MAPK signaling in HCC. Classification based on the heterogeneity of the phosphoproteome in tumors identified three distinct phosphoproteomic subtypes, each characterized by unique phosphorylation signatures, clinical characteristics, cellular signaling pathways, and kinase activities. Further validation revealed that hyperphosphorylation of SRSF3, present in the most malignant phosphoproteomic subtype, promotes cell proliferation and metastasis through the activation of SRPK1/CLKs and potential suppression of PP1 phosphatase via PPP1R7 phosphorylation. Furthermore, inhibitors targeting SRPK1 or CLKs effectively suppressed hyperphosphorylation of SRSF3-mediated migration and invasion in HCC cells. Conclusion: Our study uncovers the dysregulated phosphorylation landscapes, delineates phosphoproteomic heterogeneity in early-stage HCC, and identifies phosphorylationdependent regulatory mechanisms and key kinases with therapeutic relevance. These findings highlight the the critical role of phosphoproteomic dysregulation in driving HCC progression.