To achieve better comprehensive heat transfer performance of corrugated micro-channels, this study used 3-D conjugate heat transfer numerical method to compare cosine shaped and zigzag shaped corrugated micro-channels with secondary channels. The results indicate that reducing the wavelength of corrugated micro-channels increases the number of peaks and valleys, and significantly enhances the secondary flow intensity of the secondary channel. When the Reynolds number equals 510, the heat transfer coefficient for cosine micro-channels with wave-lengths 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 Reynolds number, but beyond a critical Reynolds number 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 wavelength of 5000 μm. However, as the wavelength decreases, the performance advantage reverses with an increase in Reynolds number. Specifically, for a wavelength of 2500 μm, the cosine type micro-channel provides optimal temperature control under low pressure drop conditions, while the zigzag type micro-channel performs better under high pressure drop conditions.