The effects of microfluidization cycles on the physicochemical properties of soy protein isolate–soy oil emulsion (SSE) films were studied. Surface weighted average diameter (d3,2), volume weighted average diameter (d4,3), and span of SSEs treated with two cycles of microfluidization were 0.78 μm, 1.21 μm, and 1.94, respectively. The d3,2, d4,3 and span of SSEs significantly decreased with increasing number of microfluidization cycles, whereas the amount of protein adsorbed on oil droplets surfaces increased according to the confocal laser scanning microscopy (CLSM) images. The CLSM and scanning electron microscopy images indicated that phase separation occurred in the SSE films treated with two cycles of microfluidization, and uniform structures gradually formed with increasing the number of microfluidization cycles. The tensile strength, elongation at break, water vapor permeability, and surface hydrophobicity of the SSE films increased with the number of microfluidization cycles, whereas the transparency values and glass transition temperatures decreased. Microfluidization decreased the discrepancy between the intensities of infrared absorption peaks of the upper and lower surfaces and reduced the amorphous structures of the SSE films.