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• Large scale all diamond microchannel has been fabricated by DC arc jet CVD and laser cutting. • Three methods have been carried out to modify the diamond microchannel surface to fulfill different terminations, including oxygen termination, hydrogen termination and fluorine termination. • The change of the surface properties of the diamond surface referring to the real situation flow was analyzed and explained in detail. The diamond microchannel heat sink (D-MCHS) has extremely ultra-high stability and heat transfer capacity, and the surface modification can further improve the heat dissipation capacity of D -MCHS. In this study, diamond microchannels were modified by three surface termination operations, including oxygen-terminated (OT), hydrogen (HT), and fluorine-terminated surfaces (FT). Referring to the real situation, after the treatment of heat flow, the hydrophobic properties of HT-diamond microchannels decreased and resulted in the increase of surface heat transfer coefficient by 11%. The hydrophilic properties of OT-diamond tend to be stable after being significantly reduced, and the heat transfer coefficient decreased by 7%. FT-diamond was the most stable; its hydrophobicity remained constant after a slight decrease in the initial stage, and the corresponding surface heat transfer coefficient increased by 14%. X-ray photoelectron spectroscopy (XPS) was used to evaluate the surface bonding state of different terminal treatments. The results show that although the F terminal has more stable hydrophobicity, its surface temperature is 5 °C higher than that of the hydrophilic terminal, and the heat transfer coefficient is reduced from 9500 to 6000 W/(m2K), decreasing by nearly 58%. [ABSTRACT FROM AUTHOR]