The invention relates to a natural sea area large-scale ecological breeding method of stichopus japonicus, belonging to the field of aquiculture. The method can realize large-scale stichopus japonicus seedling breeding at the natural sea area by the steps of selecting and culturing parent stichopus japonicus, daily management of the parent stichopus japonicus, egg taking and incubating, culturing the young, culturing young stichopus japonicus, classifying offspring seeds and temporary culturing. The method solves the problems of degraded seedling quality, reduced production quality of the seedlings, gradual increment of stichopus japonicus diseases, high energy consumption of a seedling breeding room and the like in the process of seedling cultivation in the existing artificial seedling breeding room, overcomes the technical prejudice that sea cucumber seedlings can not be cultured at the natural sea area in the traditional view, breaks through the inherent thinking set, changes the traditional production way of the artificial seedling breeding room, and can realize ecological breeding in the natural sea area. Furthermore, the method has the remarkable advantages of high survival rate, no pollution and chemical dosing as well as being nuisanceless.