The present invention relates to a method for manufacturing a composite container with different opening sizes, which is accomplished by winding with fibers impregnated with resin. First, fibers impregnated with resin are wound on a first substrate for winding a first container, wherein first openings are positioned at both ends of the first container. Then, cut the first container into two shells with a first opening each, and slip one of the shells on a second substrate. Next, fibers impregnated with resin is used for winding the second substrate and the shell such that the fibers impregnated with resin wound on the second substrate and the shell are combined to form a second container, where both ends of the second container are the first opening and a second opening with different opening sizes. Thereby, filament winding can be applied for manufacturing containers with different opening sizes on both ends, and the technique of manufacturing and performance of containers are enhanced.