Chitosan has been used for biomedical applications in recent years, primarily because of its biocompatibility. A chitosan membrane with a 30 μm thickness was prepared and investigated for its surface modification using methane ions. Methane ions were implanted into the chitosan membrane using a Kaufman ion source; bombardment was accomplished using three accelerating voltages of ion beams—30, 55, and 80 kV. The influence of the ion bombardment on morphology, crystallinity, and hydrophilicity was investigated. Attenuated total reflectance Fourier-transform infrared (ATR-FTIR) spectroscopy analysis showed that a triplet bond appeared after the implantation of methane ions (acceleration voltage: 80 kV), culminating in the creation of a more amorphous membrane structure. The analyses of atomic force microscopy (AFM) images showed that, with the increase in bombardment energy, the roughness of the surface changed. These results revealed that ion bombardment improved the hydrophilicity of the membranes and the water fluxes of chitosan membranes altered after methane ion bombardment.