Objective: We aimed to investigate the key mechanism of the DNA damage response (DDR) mutation in hepatocellular carcinoma (HCC) and construct a prognostic signature for HCC. Methods: Gene expression RNA-Seq data, somatic mutations, and clinical information were downloaded from The Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC) dataset. Using survival analysis, stromal score correlation analysis, and DDR mutation-related differential analysis, the stromal prognostic differentially expressed mRNAs in the mutation vs no-mutation group were identified. Then immune infiltration analysis, functional enrichment analysis, and prognostic risk score model construction and evaluation were carried out. Moreover, a novel prognostic nomogram was established using the risk score and independent clinical prognostic factors. Results: The proportions of resting dendritic cells and naive CD4 T cells differed significantly between the DDR mutation and no-mutation groups. Moreover, the stromal differentially expressed genes (DEGs) in the mutation vs no-mutation group were significantly enriched in DNA replication, with a significant association with DDR. Furthermore, two stromal prognostic DEGs (SCML2 and CCDC134) were identified to construct a prognostic risk model, and the risk score was confirmed as an independent prognostic biomarker in patients with HCC. The established nomogram could predict survival probability at 1, 2, and 3 years. Conclusion: Our data reveal that the DDR mutation-related stromal prognostic gene signature is associated with survival outcomes and the immune microenvironment in patients with HCC. The prognostic nomogram may help improve the clinical outcomes of patients with HCC undergoing personalized treatment.