We report the 3D microstructure analyses of natural gas hydrates sampled from Gulf of Mexico. The samples were characterized by synchrotron radiation X-ray cryo-tomographic microscopy (SRXCTM) using the ‘TOMCAT’ beam line at the Swiss Light Source (SLS). The SRXCTM demonstrates its applicability to unlock some microscopic features of the marine hydrates, in particular of crystallite size and grain boundary network. The gas hydrate domains are surrounded by a network of pores of typically a few micrometers, which are largely due to decomposition. Out of the SRXCTM data, the porosity, total volume of the voids, the void surface area and number of the total gas-filled voids have been calculated. The results reveal the capability of SRXCTM to access the 3D microstructure which is of fundamental importance to model the petrophysical properties of natural gas hydrates.