An effective zone solidification method has been found to prepare high purity Mg-Y biomaterials. The corrosion and mechanical properties of the purified middle region are improved remarkably compared with common casting method. The average gain size and secondary dendrite space decrease from the top layer to the bottom layer of the ingot. The oxides, defects and precipitates are mainly enriched in the top layer of the ingot under the impulsion of high thermal gradient. These results are in agreement with that simulated by finite elemental method using FLOW-3D software. It is confirmed that the mode of scallop symmetric solidification attributes to the purifying process. This zone solidification method not only contributes to high purity Mg-based biomaterials, but also provides a new approach to prepare high performance Mg alloys.