Mold-ripened cheese was prepared using a commercial starter culture combined with Monascus, and its physicochemical properties, free amino acids, microstructure and volatile flavor substances were evaluated. The results showed that the yield of cheese was 16.55%, and the protein, fat, calcium, water, and salt contents of the cheese were 18.03%, 33.40%, 376.67 mg/100 g, 44.47%, and 863.67 mg/100 g, respectively. During the ripening process, pH value first decreased, then increased and finally leveled off. The microstructure indicated that Monascus had a significant effect on the internal structure of mature cheese. A total of 23 free amino acids and 32 volatile compounds were identified by high performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS). At the end of the ripening period (21 days), the content of free amino acids in mold-ripened cheese was increased by an average of 58.8 times over the beginning of ripening, and the types and contents of volatile compounds also changed significantly.