o improve the quality of stirred yogurt fermented with goat milk and explore the effects of transglutaminase (TG) on the protein cross-linking degree of goat milk, stirred yogurt were treated by TG (concentrations of 1, 2, 3 u/g protein); the pH, viscosity, water holding capacity, flavor and the viable count changes in lactic acid bacteria during storage were studied and the crosslinking degree of goat milk were analyzed with SDS-PAGE electrophoresis. The results showed that the pH in storage period of yogurt was significantly higher than the control group; the viscosity and water holding capacity of stirred yogurt during storage increased significantly and the effect was more obvious with the increase of TG concentration. The contents of acetaldehyde and diacetyl decreased gradually, and the concentration of TG was greater, the effect was more obvious. TG treatment inhibited significantly the number ofStreptococcus thermophilusof stirred yogurt during storage, and with the increase of TG concentration, the content of Streptococcus thermophilus was lower, while TG treatment had no obvious effect onLactobacillus bulgaricus. SDS-PAGE revealed that  the occurrence of noticeable cross-linked on kappa-casein and alpha-lactalbumin when the goat milk treated by TG, which was beneficial to the stability of yogurt gels.