Abstract: Plant-based yogurts received widespread consumer attention due to their perceived health benefits. To investigate the effect of protein content on the quality of stirred soy yogurt and understand the relationship between microstructure and macroscopic properties such as texture and rheology, different protein content (2.5%~5.0%) bases were used in the preparation of stirred soy yogurts through fermentation and a smoothing process. The microstructure of stirred soy yogurts was characterized using laser diffraction, laser confocal microscopy and scanning electron microscopy, with subsequent analysis of the relationship between macroscopic properties and microstructure. The results showed that the microgels in stirred soy yogurt exhibited non-spherical and irregular shapes. With the increase of protein content, microgel size increased from 73.88 to 192.50 μm, accompanied by denser and more homogeneous internal structures. Additionally, the fractal dimension increased from 2.8248 to 2.8478, while the lacunarity decreased from 0.2858 to 0.2249. Meanwhile, the firmness of stirred soy yogurt increased from 23.73 to 59.69 g, the apparent viscosity (at a shear rate of 50 1/s) increased from 253.16 to 1626.67 MPa·s, and G' (at a frequency of 0.1 Hz) increased from 33.16 to 551.15 Pa. The syneresis decreased from 32.87% to 13.64%. Correlation analysis showed that microgel size and fractal dimension were positively correlated with firmness, viscosity and G', but negatively correlated with syneresis, and the lacunarity and water hole diameter were positively correlated with syneresis. This study demonstrates that protein content significantly impacts the quality of stirred soy yogurt by altering its microstructure.