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Nano-clusters based materials have received increasing attention as smart materials owing to their unique optical, electronic properties, which make their promising for a wide range of applications, such as catalysis, sensors, and drug delivery, which will expand the science of clusters. A lot of efforts have been devoted to preparing nano-scale materials with controllable size and structure in order to achieve enhanced performances in certain applications. Mass spectrometry has been widely used for characterization of clusters with different m/z . Ion mobility spectrometry combined with mass spectrometry (IM-MS) is a new technique for characterization of mental nano-clusters, which can provide the information of both structure and m/z. In this review, we compared the advantages and disadvantages between IM-MS and single crystal diffraction, nuclear magnetic resonance spectroscopy, infrared spectroscopy. The principles of different IMS including travelling-wave ion mobility spectrometry, drift tube ion mobility spectrometry and differentia mobility spectrometry were introduced. Then, the structures of different commercial IM-MS were summarized and their applications for the characterization of nanocluster were introduced, which would help to expand the ion-chemistry of atomically precise clusters. The formation of ligated metal clusters through solution-phase chemical reduction is of interest due to their sizes and structures with tunable properties. Possible isomers in ligand protected Au and Ag cluster ions have been selectively detected and identified by ion mobility mass spectrometry. The structures for vanadium oxide cluster, chromium oxide cluster, nickel oxide cluster, cerium oxide cluster, titanium oxide cluster were investigated and confirmed based on the comparisons between the measured collision cross section and the theoretical simulation. Finally, the development tendency in future were discussed and prospected. Possible tendency was suggested as following: 1) IM-MS with higher resolution should be developed to measure the size and structure of metal clusters especially for isomers. 2) For the preparation of metal cluster with size and structure selected, the clusters with special property can be obtained through the combination of IM-MS with soft deposition device, the properties of such isomers and the insights they provide on the chemistry of monolayer-protected clusters would be subjects of a future study. 3) Comparing both experimental and theoretical collision cross section would aid in characterizing clusters and exploration of the dynamic equilibrium between isomer with different structures. 4) The relationship between the structure of metal cluster and the measured reduced mobility should be investigated and the corresponding fundamental database should be set up.