A hydrothermal-modification strategy was adopted to anchor manganese oxide (MnxOy) nanoparticles over the coconut shell activated carbon (CSAC) for CH4/N2 separation. Systematic investigations were carried out to determine the effects of the type and amount of manganese salts on the adsorption performance. Dynamic breakthrough experiments showed that CSAC-KMnO4 prepared by modification with KMnO4 exhibited the optimal CH4 adsorption performance with a breakthrough time of 131 s, which was approximately 40% longer than that of pristine CSAC. At 273 K and 100 kPa, its saturated CH4 uptake was as high as 110.7 cm3 g−1, 2.92 times that of pristine CSAC. Comprehensive characterization techniques revealed that highly dispersed MnxOy nanoparticles exhibited the mixed valence states of Mn2+/Mn3+, and their abundant unsaturated coordination adsorption sites induced polarization of CH4 molecules, leading to enhanced van der Waals interaction and high adsorption capacity. Moreover, the strong oxidizing properties of Mn7+ could etch pores of the activated carbon skeleton, introducing more COOH, CO and C–O–C groups, thereby further enhancing the polarity with increased CH4 uptake. This work provides a new design pathway for highly efficient separation of CH4/N2.