Enhanced boiling heat transfer through nanofluids represents a significant approach to improving the cooling performance of electronic devices. However, the preparation of nanofluids poses challenges regarding production efficiency, morphology control, and structural stability. In addition, the underlying mechanism of flow boiling heat transfer enhancement of nanofluids, particularly changes in vapor behavior, remains a limited understanding. This study presents a facile and straightforward microfluidic strategy for the controllable synthesis of nanofluids toward efficient heat transfer enhancement. The microfluidic flow synthesis approach effectively enhances mixing efficiency at various flow rates, enabling continuous and high-throughput synthesis of boehmite nanofluids with different morphologies. The synthesized nanofluids exhibit long-term stability (>50 days) at room temperature. Both rod- and sphere-shaped nanofluids under equivalent concentrations can significantly improve critical heat flux (CHF) and maximum heat transfer coefficient (HTC) across various operating parameters, but with similar enhancement characteristics. Analysis of the period of bubble growth and burst, bubble size distributions, number of bubbles, and vapor phase fractions reveals that rod- and sphere-shaped nanofluids could shorten the period, enhance surface wetting, increase nucleation sites, and reduce bubble size efficiently and similarly. Furthermore, the effect of the concentration of nanofluid on phase-change heat transfer performance is systematically explored. 0.01 wt% nanofluid behaves the most remarkable enhancement, CHF and maximum HTC are improved by 24 % and 14.4 %, respectively. These findings not only shed new light on the controllable synthesis of functional nanomaterials but also provide important guidelines for the rational design of nanofluids for efficient two-phase cooling of electronic devices.