In order to obtain a reliable hydrophilic microstructure that can transform from the Cassie-Baxter state to the Wenzel state, a honeycomb-like microstructure was designed. It was inspired by the natural biological structure. By establishing a theoretical model of the honeycomb microstructure and using a numerical simulation program, the contact angle of the structure was predicted. Finally, a nanosecond pulsed fiber laser is used to process a honeycomb structure on the glass surface. The results show that the contact angle expression can be obtained by establishing the theoretical model of the honeycomb microstructure for the first time. The optimal boundary conditions can be obtained under the conditions of satisfying the physical constraints. The error between the predicted value of the contact angle and the measured value after processing is less than 5°. The surface contact angle decreases as the size of the honeycomb structure decreases. When the side length of honeycomb structure is about 10 μm, it reaches the super-hydrophilic state. The theoretical model of honeycomb microstructure based on wetting transition theory is feasible and can predict the surface hydrophilicity (apparent contact angle). Through nanosecond laser ablation technology assisted by light absorbing material, micron scale honeycomb structure can be accurately processed on glass surface. The honeycomb microstructure designed by bionic technology can reduce the apparent contact angle and effectively improve the hydrophilicity of glass surface.