In this study, gelatin-starch shell-yolk microspheres were prepared by water-in-water emulsion method using three different crystal types of plant rhizome starches. The microspheres were then cross-linked using chemical and natural cross-linking agents. The effects of starch crystal type and cross-linking on microsphere quality were investigated. The morphology of microspheres was spherical or nearly spherical and possessed a smooth surface. Uncross-linked microspheres had a high swelling capacity of up to about 750%. After cross-linking, the swelling of the microspheres was inhibited, and a denser structure was formed. The loading capacity of microspheres was related to their swelling capacity. The results of DSC showed that the gelatin shell of the microspheres retarded the internal starch pasting, and the thermal stability of the microspheres could be enhanced by cross-linking. Cross-linking similarly increased the resistance of the microspheres to amylase hydrolysis by about 10%. Therefore, microspheres should be cross-linked after adequate encapsulation of the cargo to obtain both high encapsulation efficiency and high stability. In addition, the microspheres prepared from three different crystal types of starch were coincidentally B + V mixed type. These results are instructive for the future utilization of such microspheres for encapsulating bioactive.