Microchannel flow boiling heat transfer with nanofluids is an effective approach to enhance the heat transfer performance of high-power electronics. However, conventional nanofluids are plagued by laborious fabrication procedures, poor stability, and uncontrollable nanoparticle sizes, which compromise the overall heat transfer efficiency. To address these challenges, a facile microfluidic synthesis strategy is developed to prepare highly stable and size-controllable silica nanofluids in a continuous, efficient, and high-throughput methodology. The introduction of silica nanofluid aims to facilitate surface bubble formation and delay coalescence, ultimately enhancing the critical heat flux (CHF) and heat transfer coefficient (HTC) for efficiently cooling silica chips. Through the specifically designed spiral microchannel reactor, nanofluids with controllable nanoparticle sizes ranging from several tens of nanometers to a few hundreds of nanometers can be synthesized with long-term (>30 days) dispersion stability at both room temperature (25 °C) and high temperature (75 °C). Importantly, with negligible changes in pressure drop, the CHF and HTC of the synthesized nanofluids increase by maximum of 55 % and 63 % respectively compared to the basic fluid. Furthermore, our results suggest that smaller-sized nanoparticles outperform larger ones at higher flow rates. These findings not only provide important guidelines for the controllable preparation of nanofluids, but also shed new light on the rational design of efficient nanosystems for two-phase cooling.