We demonstrated the DNA separation by using the three dimensional Christmas-tree nanowire chips embedded in the microfluidic system to enhance the separation range and decrease the time consuming also. We synthesize the Christmas-tree nanowire by decorating Au catalyst along the nanowires structure by sputtering and growing the branch of nanowires by Vapor-Liquid-Solid (VLS) technique as a cycle. The DNA electrophoretic mobility in the Christmas- tree nanowire decreases when the pore size between nanowire decreases by growth time. The DNA migration in the Christmas-tree nanowire chip is faster than gel electrophoresis due to the rigidity of 3D nanowire structure. Consequently, we succeeded to separate the wide range of DNA molecules by mobility difference in 3D nanowire structure in short time.