The growth-strain method was used for shape optimization of multi-connected structures. It was verified that the growth-strain method is very effective for shape optimization of structures with only one free surface to be deformed. But it could not provide reasonable optimized shape for multi-connected structures, when the growth-strain method is applied as it is. The purpose of this study is to improve the growth-strain method for shape optimization of multi-connected two- and three- dimensional structures. In order to improve, the problems that occurred as the growth-strain method was applied to multi-connected structures were examined, and then the improved method was suggested. The effectiveness and practicality of the developed shape optimization system was verified by numerical examples.