The invention discloses a method for breeding hippocampus by using a stratified net cage. The method uses the independently designed multiple-layer net cage to meet the necessary conditions of the hippocampus breeding and realize large-scale breeding of hippocampus. The method can realize the composite breeding of hippocampal seedlings, middle-aged hippocampus and parent hippocampus; the breakthrough breeding mode can reduce the technology pressures of hippocampus food supply and inflatable water body to the greatest degree, and greatly reduces the hippocampus breeding cost; at the same time, due to the very stable breeding environment and conditions, the accidental mortality of the hippocampus is reduced to a certain degree.