The invention provides an LED (Light Emitting Diode) combined chip in an array structure and a manufacturing method thereof. The combined chip comprises a plurality of GaN-based LED chips connected into a single core particle through wiring of the array structure; and each GaN-based LED chip comprises an epitaxial wafer, an insulated isolation layer, a transparent conductive layer, a P-type electrode and a P-type bonding pad, an N-type electrode and an N-type bonding pad, and a passivation layer from the bottom up in sequence. The LED combined chip is a combined device of a traditional GaN-based light emitting diode and an IC (Integrated Circuit), and is formed by integrating a plurality of traditional GaN-based LED chip units in an array type; and the chip units form a single core particle, so that the amount of user packaging and wire bonding is greatly reduced, and the packaging difficulty is reduced. Moreover, the combined chip works in a driving manner of high current and small voltage, the stress caused by thermal mismatch and lattice mismatch is relieved, and the light extraction efficiency is increased because of the increase of side wall area, so that the luminescence efficiency is improved.