In this study, the native acid protease gene in Yarrowia lipolytica 22a-2 with high content of protein was disrupted, and the disruptant 3-13-10 obtained had very low acid protease activity. Then, the acid protease gene (AP1 gene) from Saccharomycopsis fibuligera A11 was actively expressed in the disruptant 3-13-10, and the transformant 43 carrying the AP1 gene had high specific acid protease activity (46.7 U/mg). The recombinant acid protease produced by the transformant 43 was found to be able to actively clot milk, and the transformant 43 still kept high content of protein. The hydrolysis products of kappa-casein under catalysis of the recombinant acid protease and the commercial calf rennet had the same molecular mass, suggesting that the recombinant acid protease and its producer can be used both in cheese manufacturing and as protein source in food industry.