Medulloblastoma is the most common malignant pediatric brain tumor. These tumors have considerable intratumoral and intertumoral heterogeneity. Recent advancements in single-cell multi-omics technologies have provided unprecedented insights into the cellular and molecular landscapes of medulloblastoma, enabling the identification of novel therapeutic targets and improving our understanding of tumorigenesis and disease progression. This chapter outlines essential protocols for multi-omics analyses of medulloblastoma. Utilizing a dataset from a recent multi-omics study on human medulloblastoma samples, we describe the framework for performing single-cell transcriptomics, genomics, and chromosomal interaction analysis and data-driven integration to identify the molecular networks underlying disease pathogenesis. This protocol highlights the profound impact of multi-omics technologies on our understanding of various aspects of pediatric brain tumors, including tumor lineage evolution, activated molecular pathways, cancer genetics and epigenetics, and the identification of potential therapeutic targets.