The present invention relates to a method of preparing a delivery system capable of loading bioactive growth factors that are essential for the differentiation and proliferation of cells and is characterized as loading at least two types of components comprising growth factors in a single carrier, whereby the release of each of the plurality of growth factors can be temporally controlled. Specifically, the method of preparing a microcapsule type growth factor delivery system according to the present invention includes: (1) preparing a polymeric microsphere comprising a first component, and then encapsulating the microspheres by electrodropping the polymer microsphere into another polymer comprising a second component, thereby manufacturing a core-shell structured, microcapsule type delivery system, or (2) encapsulating a polymer solution comprising a first component by electrodropping the polymer solution into another polymer comprising a second component, thereby manufacturing a core-shell structured microcapsule type delivery system. The present invention also provides a stem cell differentiation method involving bringing a microcapsule type delivery system loaded with multiple growth factors according to the present invention into contact with stem cells.