The differences in characteristics between stirred and set yogurt produced from A1 or A2 β-casein milk were studied. The water-holding capacity of stirred and set yogurt produced from A1 β-casein milk was greater than 69%, and the water-holding capacity of stirred and set yogurt produced from A2 β-casein milk was greater than 65%. Textural analysis showed that the hardness and consistency of set yogurt produced from A1 β-casein milk were 41.4% and 59.8% higher than those of set yogurt produced from A2 β-casein, respectively. Compared with A2 β-casein yogurt, A1 β-casein yogurt had better viscosity. The results of rheology and microstructure showed that the hysteresis loop area of A1 β-casein yogurt was 14.6% smaller than that of A2 β-casein yogurt indicating that the former’s structure can be more easily damaged and its network structure is sparser. This study provides theoretical support for the application of A2 β-casein milk in yogurt.