The invention provides a flip LED chip structure and a manufacturing method thereof. The flip LED chip structure comprises a three-dimensional graphic structure, a sapphire substrate, a semiconductor material layer, an N electrode, a contact reflective layer, an insulating isolation layer, a P electrode and a welding electrode 10, wherein the semiconductor material layer comprises an N-type semiconductor material, a light-emitting layer and a P-type semiconductor material. The manufacturing method comprises the steps of: forming a mask material on the surface of the sapphire substrate, manufacturing a photoresist pattern on the mask by adopting a photoetching method, etching the mask, removing a photoresist, forming a three-dimensional graphic structure mask layer on the surface of the substrate, forming the three-dimensional graphic structure on the surface of the substrate, and eliminating the mask finally. According to the flip LED chip structure and the manufacturing method thereof, the light emergent surface of the sapphire substrate of the flip LED chip can be designed and processed optically according to light source requirements of a specific application scene, and the single, periodic or non-periodic three-dimensional graphic structure can be manufactured, thereby realizing the needed light source requirements.