A manufacturing method of a minute structure having fine structures on opposing inner surfaces, includes the steps of forming a first pattern in a surface of a first layer, forming a sacrificial layer on the patterned surface of the first layer, forming a second pattern on a surface of the sacrificial layer, forming a second layer on the sacrificial layer and a portion of the surface of the first layer, and removing a member constituting the sacrificial layer. In the step of forming the first pattern on the first layer and the step of forming the second pattern on the sacrificial layer, the patterns are formed using the same alignment marks as references. This manufacturing method can realize highly accurate alignment even when plural lenses or DOEs are used.