The invention provides a method for producing an algae enzyme through double-term fermentation. According to the method, one or multiple of brown algae, red algae and green algae and other large algae are used as the basis, processes such as crushing, homogenizing, heating and pH regulation are adopted, the edible bacillus subtilis is subjected to first-term fermentation and the edible lactobacillus plantarum is subjected to second-term fermentation, and therefore, the high-activity enzyme components such as protease and amylase and special biological active substances such as algae active oligosaccharides can be produced; the taste of the algae and the digestibility are particularly improved, and as a result, the high-quality algae enzyme is produced.