Using commercial calf rennet as the control, fresh cheese was processed with milk-clotting enzyme from germinated moringa seed. The sensory attributes, nutritient components, functional properties (stretchability, melting, oil precipitation), total color difference, free fatty acids and other indicators were compared and analyzed. The results showed that there was no significant difference in sensory attributes, yield, protein content and total color difference ΔE value between the two processed cheeses (P>0.05). The fat content of the cheese processed with milk-clotting enzyme from germinated moringa seed was 17.71%, which was significantly lower than that of processed cheese with calf rennet (P<0.05). The meltability and tensile length of the processed cheese obtained with milk-clotting enzyme from germinated moringa seed were 14.50 mm and 30.40 cm, respectively, which were significantly better than those of calf rennet processed cheese (P<0.05). There was no significant difference in the total content of free fatty acids between the two types of processed cheese (P>0.05). The mass fraction of linoleic acid in the processed cheese prepared with milk-clotting enzyme from germinated moringa seed was 1.68%, which was significantly higher than that of the processed cheese prepared with calf rennet. This study showed that the milk-clotting enzyme from germinated moringa seed can replace calf rennet to a certain extent in the processing of fresh cheese, which provides an important reference value for the application of milk-clotting enzyme from germinated moringa seed in cheese processing.