This study aims to comprehensively explore the physicochemical, nutritional and biological properties of whole soy milk yogurt, which depend on the bacterial strains used. All fermented samples demonstrated a significant increase in active ingredient content, and reduced anti-nutritional factors. Fermentation significantly enhanced the antioxidant, hypoglycemic, hypolipidemic, and hypotensive abilities of whole soy milk yogurt, effectively enhance flavor characteristics, improve color, and increase consumer preference. Samples fermented with Lactobacillus acidophilus have a moderate water holding capacity (76.72 +/- 1.10%) and viscosity (1420.00 +/- 30.41 cP), a stable microstructure, and a better texture and taste; they are more favored by consumers and have received the highest sensory evaluation score of 78.33. The commercial culture fermented samples contained a high level of active substances along with robust antioxidant, hypoglycemic, and hypolipidemic abilities. Principal component analysis results indicated the commercial culture fermented sample achieved the highest composite score (3.70), thus making it a more suitable choice for this fermentation process. This study prevents resource waste and environmental pollution in the traditional process of preparing fermented soy milk and provides a theoretical basis for selecting suitable strains for the fermentation of whole soy milk yogurt.