The damage in germanium (Ge) optical window irradiated by a near-infrared continuous wave (CW) laser was studied. Laser-induced heating and melting process were surveyed, and the specific laser power and the irradiance time to melt were estimated by numerical simulation. The experiments were also carried out to investigate the macro and micro structure change on Ge window. Results showed that the surface deformation was formed by melting and resolidification process, the damaged surface had a polycrystalline phase, and the transmittance as an optical performance factor in mid-infrared region was decreased. We confirmed that an abnormal polycrystalline phase and surface deformation effect such as hillock formation and roughness increase reduced the transmittance of Ge window and were the damage mechanism of CW laser induced damage on Ge window.