Microfluidic technology, as a continuous and mass preparation method of nanoparticles, has attracted much attention in recent years. In this study, zein nanoparticles (ZNPs) were continuously fabricated in a highly controlled manner by combining a microfluidics platform with the antisolvent method. The impact of ethanol content (60~95%, v/v) and flow rates of inner and outer phases in the microfluidics platform on particle properties were examined. Among all ZNPS, 90%-ZNPs have the highest solubility (32.83%) and the lowest hydrophobicity (90.43), which is the reverse point of the hydrophobicity of ZNPs. Moreover, when the inner phase flow rate was 1.5 mL/h, the particle size decreased significantly from 182.81 nm to 133.13 nm as the outer phase flow rate increased from 10 mL/h to 50 mL/h. The results revealed that ethanol content had significant impacts on hydrophilic–hydrophobic properties of ZNPs. The flow rates of ethanol–water solutions and deionized water (solvent and antisolvent) in the microfluidics platform significantly affected the particle size of ZNPs. These findings demonstrated that the combined application of a microfluidics platform and an antisolvent method could be an effective pathway for precisely controlling the fabrication process of protein nanoparticles and modulating their physicochemical properties.