Nitrogen-containing heterocycles are especially considered "privileged" structural scaffolds for the development of new drugs. However, traditional methods of organic synthesis are mainly based on thermal cycloaddition reaction; thus, the exploration of new strategies for the rapid assembly of N-heterocycles under mild conditions is highly desirable. Here, we developed a new method that visible light along with 1 mol % cercosporin, which is one of the perylenequinonoid pigments with excellent properties of photosensitization and can be easily produced by a new isolated endophytic fungus Cercospora sp. JNU001 strain with high yield through microbial fermentation, catalyzes the synthesis of 1,2,3-thiadiazoles and 1,4,5,6-tetrahydropyridazines by a photocatalytic process with good regioselectivity and broad functional-group compatibility under mild conditions. Thus, a bridge between microbial fermentation and organic photocatalysis for the construction of nitrogen-containing heterocycles was set up in a sustainable, environmentally friendly manner.