The study of the influence of the nanoparticle volume fraction and aspect ratio of microchannels on the fluid flow and heat transfer characteristics of nanofluids in microchannels is important in the optimal design of heat dissipation systems with high heat flux. In this work, the computational fluid dynamics method was adopted to simulate the flow and heat transfer characteristics of two types of water–Al2O3 nanofluids with two different volume fractions and five types of microchannel heat sinks with different aspect ratios. Results showed that increasing the nanoparticle volume fraction reduced the average temperature of the liquid–solid heat transfer surface and thereby improved the heat transfer capacity of the nanofluids. Meanwhile, the increase of the nanoparticle volume fraction led to a considerable increase in the pumping power of the system. Changing the aspect ratio of the microchannel effectively improved the heat transfer capacity of the heat sink. Moreover, increasing the aspect ratio effectively reduced the average temperature of the heating surface of the heat sink without significantly increasing the flow resistance loss. When the aspect ratio exceeded 30, the heat transfer coefficient did not increase with the increase of the aspect ratio. The results of this work may offer guiding significance for the optimal design of high heat flux microchannel heat sinks.