Metal-organic frameworks have been largely investigated as gas adsorbent materials in the past two decades. With deep investigation of crystallography, the rational adjustments of SBUs, linker geometry, linker length, functional groups and guest molecules, the size, shape, and internal surface property of MOFs can be tuned. One of the hottest topics for the application of this type of high porous material is the gas storage and separation, especially for hydrogen and methane, which are two gases with high specific energy. In this critical review, we highlight the design strategies of MOFs through three aspects: the SBUs, linkers and post-synthesis. Then we review the recent progress of MOFs in the storage and separation of hydrogen and methane. Examples of the functional designed MOFs for storage or separation of hydrogen and methane are described respectively.