Abstract: Single-cell sequencing is characterized by precise analysis of genome, transcriptome, epigenomics, and multi-omics of cancer cells at the single-cell level, which promotes understanding of evolution and dynamic changes in cancer niches. Yet, intra- and extra-tumor heterogeneity of brain tumors can make it difficult to obtain a full-view landscape in bulky tumor assessment. Based on single-cell sequencing, genomic instability, biomarker, signaling pathway and immune responses in the tumor environment of a brain malignant tumor can be uncovered, which provides a novel opportunity for assessment, diagnosis, classification and management of brain malignant tumors. In this article, we review the progress of single-cell sequencing and the prospect in the management of brain malignant tumor in the future.