Heat transfer and hydrodynamic performances for nanofluids, Al2O3‐water and SiO2‐water, are numerically investigated with different nanoparticles’ volume fractions and the initial velocities in a fractal microchannel heat sink. The fractal microchannel is 100 μm × 100 μm in the inlet cross‐section, and the length at the 0th level is 2000 μm. A constant heat flux of 500 kW/m2 was applied to the bottom wall of the fractal microchannel heat sink. The heat transfer and hydrodynamic performances of different cases are discussed in terms of the mean heat transfer coefficient, mean base temperature, pressure loss, thermal resistance, friction factor f/f0, and COP/COP0. Results indicate that increasing the initial velocity and nanoparticles’ volume fraction lead to an enhanced heat transfer at the expense of pressure loss. Al2O3‐water has a higher mean heat transfer coefficient and pressure drop than that of SiO2‐water, a lower f/f0, mean base temperature, thermal resistance, and COP/COP0. Ultimately, as compared to pure water, the heat transfer coefficients of 4% Al2O3‐water increased by 7.53%, 7.80%, 8.00%, 8.14%, 8.16%, and 8.30%, and the pressure drops increased by 32.09%, 31.41%, 30.81%, 30.05%, 29.21%, and 28.58%, respectively, corresponding to the initial velocities by 4, 5, 6, 7, 8 and 9 m/s.