To achieve better comprehensive heat transfer performance of corrugated microchannels, this study used three-dimensional conjugate heat transfer numerical method to compare cosine shaped and zigzag shaped corrugated microchannels with secondary channels. The results indicate that reducing the wavelength of corrugated microchannels increases the number of peaks and valleys, and significantly enhances the secondary flow intensity of the secondary channel. When the Re equals 510, the heat transfer coefficient for cosine microchannels with wavelengths of 2500 μm and 1250 μm increases of 47% and 127% compared to that with wavelength of 5000 μm. The heat transfer characteristics of cosine channels outperformed zigzag channels at lower Re, but beyond a critical Re of ~680, the zigzag geometry with wavelengths of 2500 μm and 1250 μm exhibited a superior heat transfer coefficient and a lower thermal resistance. The performance evaluation shows that cosine channels have better overall thermal performance at a wavelngth of 5000 μm. However, as the wavelength decreases, the performance advantage reverses with an increase in Re. Specifically, for a wavelength of 2500 μm, the cosine type microchannel provides optimal temperature control under low pressure drop conditions, while the zigzag type microchannel performs better under high pressure drop conditions.