The electronic properties of wurtzite/zinc-blende (WZ/ZB) heterojunction GaN are investigated using first-principles methods. A small component of ZB stacking formed along the growth direction in the WZ GaN nanowires does not show a significant effect on the electronic property, whereas a charge separation of electrons and holes occurs along the directions perpendicular to the growth direction in the ZB stacking. The later case provides an efficient way to separate the charge through controlling crystal structure. These results have significant implications for most state of the art excitonic solar cells and the tuning region in tunable laser diodes.