The investigation about chromatin 3D structure is becoming one indispensable way in studying genome functions and gene regulation. In past several years, thanks to the development of chromatin conformation capture technology and decreasing cost of high throughput sequencing, the amount of whole-genome interaction data increases rapidly with the ascending resolutions. This not only brought the chances for interpreting 3D genome, but also challenged the modeling methods. Nowadays, methods of analyzing these data covered a wide range, including pre-processing, normalization, visualization, features extraction and 3D modeling; however, choosing efficient and precise computational methods becomes an obstacle limiting the study of 3D genome. In this paper, we sum up these methods according to their suitable conditions, principles and characters and focus on the methods for new technologies and requirements in order to promote the application and development of these methods, assisting the investigation of 3D genome.