The present invention relates to a heterogeneous substrate, to a nitride-based semiconductor device using the same and to a manufacturing method thereof. The present invention adjusts the mode of crystal growth to form a high quality non-polar or semi-polar nitride layer on a non-polar plane or a semi-polar plane of the heterogeneous substrate. The method according to the present invention prepares a base substrate having either a non-polar plane or a semi-polar plane, and forms a nitride-based crystal growth core layer on the plane of the prepared base substrate. A first buffer layer is grown on the crystal growth core layer such that the first buffer layer is grown faster in a vertical direction than in a horizontal direction. A horizontal growing layer is grown on the first buffer layer such that the horizontal growing layer is grown faster in a horizontal direction than in a vertical direction. Subsequently, a second buffer layer is grown on the horizontal growing layer. Here, a nitride silicon layer having a plurality of holes can be further formed between the horizontal growing layer on the first buffer layer and the second buffer layer.