The invention provides a composite patterned substrate using a low-refractive index material as a medium and a manufacturing method thereof. The manufacturing method comprises the following steps: S1,a sapphire substrate is provided, and a low-refractive index medium layer is deposited on the surface of the sapphire substrate, wherein the refractive index of the low-refractive index medium layeris smaller than 1.8; S2, the low-refractive index medium layer is etched to obtain a depressed structure, and the depressed structure exposes the sapphire substrate; and S3, an AlxGa1-xN buffer layergrows on the surface of the sapphire substrate exposed in the depressed structure to obtain a composite patterned substrate, wherein 0< / =X< / =1. The composite patterned substrate reduces refraction oflight inside the chip, light reflection is improved, the extraction efficiency of an LED chip is improved, the production efficiency can be improved, and the production cost is reduced.