<p>Three-dimensional (3D) chromatin structure is crucial for gene regulation and cellular identity, with alterations in this structure being closely associated with tumor development. Although the research of tumor genomics has made significant progress in the past decade, the mechanism of 3D chromatin structure in tumorigenesis is not completely clear. Recent studies have shown that the distortion of chromatin spatial conformation has become one of the core factors driving normal cell carcinogenesis by changing the gene regulatory network. Abnormal high-order chromatin organization leads to abnormal activation of oncogenes or silencing of tumor suppressor genes. This 3D chromatin disorder has been confirmed to be directly related to the phenotypic plasticity of a variety of tumors. Therefore, the dynamic changes of 3D chromatin structure play a key role in the occurrence and development of tumors, especially for malignant tumors with difficult diagnosis and lack of treatment. This article provides an overview of hierarchical alterations in cancer 3D chromatin structure, the mechanisms governing these changes, recent advances in detection technologies, and emerging therapeutic strategies. The unique 3D chromatin variation pattern in cancers may become a new biomarker and provide a theoretical basis for epigenetic therapy targeting chromatin spatial organization. In the future, integrating multi-omics data to develop specific drugs for key nodes of the 3D chromatin and establishing an early diagnosis system based on spatial chromatin characteristics will become an important direction to break through the bottleneck of cancer treatment.</p>