To explore changes of the ripening properties of goat milk cheese made with Bacillus amyloliquefaciens GSBa-1 rennet (cheese B), commercial rennet and cheese prepared with the same batch of goat milk (cheese A) were used as the control group. Changes in main components, texture properties, microbial indicators and flavor substances were analyzed during the 60-day ripening of cheeses. The results showed that there was no significant difference in the cheese yield between the two groups. The moisture, protein and fat contents of cheese increased first and then decreased, and contents of cheese B were always higher than those of cheese A. The total contents of free amino acids increased first and then decreased, and the contents of phenylalanine, aspartic acid, isoleucine, methionine and serine in cheese B were higher than those of cheese A. The texture characteristics of cheese B in the early stage of ripening were better than cheese A. The number of Lactococcus lactis of cheese A increased by (5.22±0.02)% after ripening, and cheese B did not change significantly(P>0.05). During cheese ripening, the types and contents of volatile flavor substances in the two groups of cheese increased, but the nonanoic acid, octanol, 2-heptanone, 2-nonanone and dimethyl sulfone formed by cheese B gave goat milk cheese unique and rich flavor. Therefore, GSBa-1 rennet had the potential to replace commercial rennet in the production of goat milk cheese, and could promote the formation of cheese flavor and the improvement of quality.