An effective method denoted as “center of mass probability distributions” was employed to study the methane adsorption mechanism in metal-organic framework PCN-14 which shows the highest methane storage capacity to date, finding that this material has two adsorption sites for methane molecules, and the organic linkers play an important role in adsorption. Thus, a new material named PCN-M was designed by modifying the organic linkers of PCN-14. The newly designed MOF material has a methane storage capacity of ca. 257 V/V at 290 K and 3.5 MPa, which is 12% higher than that of PCN-14. On the other hand, it has a methane capacity of ca. 241 V/V at 298 K and 3.5 MPa, which is 34% over the DOE target (180 V/V). In addition, this work shows that a rational modification of the organic linkers is a feasible way to improve the methane storage capacity, providing helpful information for future MOF design.