In this paper, the following contents including the original receptor EI213 and other two control materials, RAPD polymorphism, photosynthetic efficiency, and the number of vascular bundles of the first internodes below the peduncle have been studied for the eight F7 transgenic lines obtained from ion beam implantation. The results showed that there was a significant variation in genomes of maize-rice line, compared with the receptor EI213, after the total exogenous maize DNA was introduced into EI213. The number of the vascular bundles of maize-rice progenys lines was obviously much larger than those of the original receptor EI213 and other two controls GER-3 and MH63, and along with the photosynthetic efficiency of maize-rice progenys lines being gone up. Moreover, the parenchyma cells around the vascular bundles of the transgenic lines became much larger in number and in size than those around the controls. All these indicated that the maize-rice progenys lines are really different from and superior to the receptor and the controls. It is a novel and useful way to apply ion beam implantation in transferring DNA from C4 plant maize into C3 plant rice.