More than half of patients with hepatocellular carcinoma (HCC) have multiple lesions in the liver at the time when they attend the hospital, and there are limited treatment methods with poor efficacy for multifocal HCC in clinical practice. The high degree of tumor heterogeneity in multifocal HCC is the leading cause of treatment failure. More and more studies use multi-omics sequencing to explore the heterogeneity between different lesions at the genetic and transcriptional levels, including tumor clonal evolution, gene mutations, copy number variations, structural variations, RNA expression, and tumor immune microenvironment. Drug target distribution shaped by clonal evolution and the characteristics of immune microenvironment can accurately predict the response to targeted drugs and immunotherapy in patients with multifocal HCC. Therefore, a comprehensive and accurate assessment of the heterogeneity of multifocal HCC based on a multi-omics study is of vital importance in the implementation of precise treatment.