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Hepatocellular carcinoma (HCC) is a major cause of cancer-related death worldwide. Although the nucleolar protein NOL12 has been implicated in HCC progression, its comprehensive expression patterns, clinical significance and regulation-particularly the potential involvement of miR-1246-5p and H3K27ac-are not fully understood, warranting further investigation. To analyse the expression pattern and clinical significance of NOL12, we integrated bulk RNA sequencing (bulk RNA-seq) data (4264 HCC cases vs. 3145 non-HCC cases), single-cell RNA sequencing (scRNA-seq) data (12 HCC samples) and spatial transcriptomics (ST) data from public databases including GEO, TCGA and GTEx. This integration was combined with in-house immunohistochemistry (IHC) data from 394 pairs of HCC tissues and adjacent non-tumour tissues. CRISPR screening was used to assess the effect of NOL12 depletion on HCC cell proliferation. Seven immune infiltration analysis methods (including CIBERSORT) were applied to the TCGA-GTEx dataset to explore the association between NOL12 and the tumour immune microenvironment (TME). Gene ontology (GO) enrichment, Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway and Gene Set Enrichment Analysis (GSEA) were performed based on NOL12-associated genes involved in HCC initiation and progression. Additionally, chromatin immunoprecipitation sequencing (ChIP-seq) data from Cistrome DB were used to predict and construct the miR-1246-5p-enhancer-NOL12 regulatory network. Potential high-affinity drug molecules targeting NOL12 were screened via the Cancer Therapeutics Response Portal (CTRP) database and molecular docking. Multi-dimensional analysis revealed significant upregulation of NOL12 in HCC (SMD = 0.64, 95% CI: 0.42-0.85; sROC AUC = 0.79). IHC validation confirmed higher NOL12 expression in HCC tissues (p < 0.0001, ROC AUC = 0.665). CRISPR screening showed that NOL12 depletion inhibited HCC cell proliferation. Mechanistically, NOL12 was enriched in the spliceosome pathway. ChIP-seq identified an H3K27ac-modified enhancer in the NOL12 promoter overlapping with miR-1246-5p binding sites, and miR-1246-5p expression positively correlated with NOL12 (r = 0.43, p = 0.018). Drug sensitivity prediction analysis showed that NOL12 protein exhibited significant sensitivity to BRD-K71781559, MST-312, IU1, BRD9876 and PRL-3 inhibitor I, with favourable binding energies. NOL12 may be regulated by the putative miR-1246-5p/H3K27ac enhancer axis and promotes HCC progression through the spliceosome pathway, supporting its potential as a novel therapeutic target for HCC.