AbstractHepatocellular carcinoma (HCC) remains a crucial public health problem around the world, and the outlook remains bleak. More accurate prediction models are urgently needed because of the great heterogeneity of HCC. The S100 protein family contains over 20 differentially expressed members, which are commonly dysregulated in cancers. In the present study, we analyzed the expression profile of S100 family members in patients with HCC based on the TCGA database. A novel prognostic risk score model, based on S100 family members, was developed using the least absolute shrinkage and selection operator regression algorithm, to analyze the clinical outcome. Our prediction model showed a powerful predictive value (1-year AUC: 0.738; 3-year AUC: 0.746; 5-year AUC: 0.813), while two former prediction models had less excellent performances than ours. And the S100 family members-based subtypes reveal the heterogeneity in many aspects, including gene mutations, phenotypic traits, tumor immune infiltration, and predictive therapeutic efficacy. We further investigated the role of S100A9, one member with the highest coefficient in the risk score model, which was mainly expressed in para-tumoral tissues. Using the Single-Sample Gene Set Enrichment Analysis algorithm and immunofluorescence staining of tumor tissue sections, we found that S100A9 may be associated with macrophages. These findings provide a new potential risk score model for HCC and support further study of S100 family members in patients, especially S100A9.