Introduction of hierarchical microstructures nowadays is considered as an important method to create superhydrophobic surfaces, but the majority of current studies mainly focus on arbitrary or simple 3D geometries. Therefore, only statistic results or particular conclusions can be obtained. Given this concern, two‐photon polymerization (TPP) is applied to create well‐defined 3D microstructures with high resolution, including fractal Sierpinski tetrahedrons, and hierarchical pyramid structures. Surfaces that have fractal structures with higher complexity are found to be more hydrophobic than their lower‐stage counterparts. Additionally, fractal Sierpinski tetrahedron structures prove to possess higher efficiency in achieving superhydrophobicity when compared to hierarchical pyramids. Further, TPP is also adopted in creating microstructures on flexible substrates. As a demonstration, an array of hierarchical pyramids is fabricated on a plastic film, and superhydrophobicity still remains even after 100 times of bending and relaxing. Moreover, owing to the convenience of spatial control from TPP, tuning of wetting performance in different regions of surfaces is achievable. With this technique, the role of the fractal and hierarchical microstructures in flexible natural creatures can be better understood, thus facilitating the applications, for which robust wetting control is required.