The invention discloses a centrifugal micro-fluidic chip as well as a manufacturing method and an application method thereof. The centrifugal micro-fluidic chip comprises a bearing substrate and a micro-fluidic substrate as well as an image collecting device, wherein the bearing substrate comprises multiple super lens arrays; and the micro-fluidic substrate comprises multiple cell catching cavities, and the cell catching cavities and the super lens arrays are arranged in one-to-one correspondence. Sorting operation is carried out on cells through the multiple cavities on the micro-fluidic substrate, and after the cells are captured, the cells are imaged through super lenses and the image collecting device, so that the centrifugal micro-fluidic chip has the functions of cell sorting, high resolution cell imaging and the like. According to the centrifugal micro-fluidic chip, bonded assembly is carried out on the bearing substrate manufactured with a nano-sized process and the micro-fluidic substrate manufactured with a micro-sized process, and a simple micro and nano cross-scale machining process is provided, so that the super lenses can be integrated on the centrifugal micro-fluidic chip, and accordingly, a high-efficiency high-precision cell operation analysis tool is provided for cytomechanics research.