The regulation of energy release characteristics and safety of highly active metal fuels has attracted significant attention. In response to the limitations of using hydrofluoric acid (HF) to modify zirconium (Zr) powder in batch reactors, a microfluidic method coupling ultrasound and coaxial flow microreactors was proposed to achieve the control of the microstructure on the surface of Zr powder. The fluid flow and mixing characteristics in the microreactor were analyzed using on-line detection devices, leading to the determination of suitable fluid parameters. Through analysis of the reaction process between Zr and HF, a reaction model based on the HF concentration was established and subsequently verified through a microreaction system. The results indicate that the HF concentration greatly influences the morphology and composition of Zr powder, thereby determining the material and structural transformation of the Zr powder surface. The excellent thermal oxidation performance and electrostatic safety of HF-modified Zr powder were confirmed through thermal analysis and electrostatic discharge sensitivity tests. This study provides valuable insights for controlling the microstructure and properties of ultrafine Zr powder.