In the present study, we used a microfluidic system for studying the combined effects of thigmotaxis and rheotaxis for sperm separation process to achieve the successful Assisted reproductive technology (ART). The designed PDMS-based microfluidic system had four various geometries, including linear, square, zigzag, and sinusoidal. The functionality of separated sperm was evaluated by sperm tracking (ImageJ), motility assay (CASA software), and morphology assay (Papanicolaou ultrafast staining). Probing various geometries revealed 100% motility. In non-linear geometries, sperm's periodic detachment from the walls gave rise to the periodic interaction with the high flow velocity in the center of the channel, resulting in the separation of high-quality sperm with progressive motility. The collected data proved the influence of thigmotaxis on the quality of separated sperm. Morphologically improvement in separated sperm from the sinusoidal geometry was significant than others, which means the sinusoidal structure would be the best candidate for the sperm separation process. The online version contains supplementary material available at 10.1007/s13534-023-00294-8.