As core parts of microfluidic chip analysis systems, micromixers show robust applications in wide fields. However, restricted by the fabrication technology, it remains challenging to achieve high-quality micromixers with both delicately designed structure and efficient mixing. In this study, based on the theory of chaotic mixing, sinusoidal structures with variable phases were designed and then fabricated through scanning probe lithography (SPL) and post-selective etching. It was found that scratches with phase differences can lead to the periodic formation of amorphous silicon (a-Si), which can resist etching. Consequentially, misaligned sine channels with thick-thin alternating 3D shapes can be generated in situ from the scratched traces after the etching. Further analysis showed that a thicker a-Si layer can be obtained by reducing the line spacing in the scratching, confirmed by Raman detections and simulations. With the proposed method, the misaligned sine micromixer was achieved with higher mixing efficiency than ever. The duplicating process was also investigated for high-precision production of micromixers. The study provided strategies for the miniaturization of high-performance microfluidic chips.