Objective <p>We aimed to examine the panoramic cellular composition and spatial structure of clinical samples from nonalcoholic fatty liver disease-associated hepatocellular carcinoma (NAFLD-HCC), assess the landscape of the tumor microenvironment (TME) and identify potential clinical biomarkers for prognosis.</p> Methods <p>Imaging mass cytometry (IMC) technology was used to analyze biomarker expression and spatial distribution in samples from 56 patients with NAFLD-HCC. Thirty-seven distinct metal-conjugated antibodies were designed to label the tumor, border and adjacent tissue regions, producing 367 highly multiplexed histological images at single-cell resolution. By combining biomarker expression levels with relative cell positional relationships, we defined functional units as tightly interacting cellular neighborhoods (CNs). Univariate and multivariate Cox regression models were employed to identify independent risk factors for prognosis assessment in patients with NAFLD-HCC on the basis of the proportion of CNs and other conventional clinical indicators.</p> Results <p>Eighteen clusters of cells and 9 CNs were defined. Heterogeneity in the TME and CN composition was observed not only across various regions within the same individual but also among comparable regions in different patients. Overall survival data revealed that patients with high enrichment of GPC3⁺/YAP⁺ cancer cell-associated CNs had poor clinical prognoses.</p> Conclusion <p>Our study provides a landscape of NAFLD-HCC and its TME characteristics from a topological perspective. These findings indicate that targeting GPC3⁺/YAP⁺ cancer cells may improve the long-term prognosis of patients with NAFLD-HCC.</p>