An effective method denoted as "computer tomography for materials" (mCT) was employed to study the adsorption sites inside metal-organic frameworks (MOFs) at any positions and any view angles. For MOF-5, the first adsorption site alpha(-COO)(3) was clearly observed from the mCT images; it locates at the position where three -COO groups joined like a cup. There are four alpha(-COO)(3) sites around the Zn4O cluster. Two of them located at the diagonal of the Zn4O cluster are in the same plane "A", whereas the other two equivalent adsorption sites are in another plane "B", which is about 5.4 angstrom away from the plane A. It was found that the electronegativity of oxygen atoms is very important to the adsorption of hydrogen molecules. The hydrogen amount adsorbed in MOFs might be enhanced by introducing some strong electronegative atoms to the organic linkers or frameworks. On the basis of this point of view, five new MOF materials were designed. The adsorbed amounts both in number of hydrogen molecules per unit cell and weight uptake for all of the designed MOFs were calculated. The adsorption amounts of designed MOFs were improved, and the amount for MOF-d5 at 1 bar is as high as 3.7 wt %. It is nearly 5-6 times of that of MOF-5 as a whole. It can be observed that extra adsorption sites were formed in the pores and the effective occupation rate of pore space was obviously improved viewing from the mCT images. These results may give helpful suggestions for the synthetic experimentalists.