Set yogurt's physical characteristics are greatly affected by the homogenization and heat treatment processes. In our previous study, set yogurt treated at 130°C and with the fat particle size reduced to ≤0.6 μm had equivalent curd strength, less syneresis and smoother texture than yogurt treated at 95°C. When investigating the mechanisms underlying yogurt's physical properties, it is important to evaluate the yogurt's microstructure. We conducted electron microscopy evaluations to investigate the mechanisms of changes in yogurt's physical properties caused by 130°C heat treatment and by a reduction in the fat globule size. We prepared yogurt mixtures by combining heat treatment at 95 and 130°C and homogenization pressure at 10 + 5 and 35 + 5 MPa and then fermented the mixtures in a common yogurt starter. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were used for the structural observations. Fine particles were observed on the surface of the casein micelles of the yogurt treated at 95°C, and the coalescence density between micelles was high. The surface of the yogurt treated at 130°C had few fine particles, and the coalescence density between micelles was low. The yogurt treated at 130°C with 35 + 5 MPa homogenization had low coalescence density between casein micelles, but smaller-particle-size fat globules increased the network density. Approximately 30% of the fat globules were estimated to be incorporated into the yogurt networks compared to the volume of casein micelles. We speculate that 130°C heat treatment alters the structure of whey protein on the surface of casein micelles and interferes with network formation, but reducing the size of fat globules reinforces the network as a pseudoprotein.