The fabrication of a highly ordered novel ZnO/Si nano-heterojuntion array is introduced. ZnO seed layer is first deposited on the Si (P<111>) surface. The nucleation sites are then defined by patterning the surface through focused ion beam (FIB) system. The ZnO nanorods are grown on the nucleation sites through hydrothermal process. The whole fabrication process is simple, facile and offers direct control of the space, length and aspect ratio of the array. It is found that ZnO/Si nanojunctions show an improved interface when subjected to heat treatment. The recrystallization of ZnO and the tensile lattice strain of Si developed during the heating process contribute the enhancement of their photoresponses to white light. The photoluminescence (PL) measurement result of nano-heterojunction arrays with different parameters is discussed.