A separation type unit pixel of an image sensor, which can control light that incidents onto a photodiode at various angles, and be suitable for a zoom function in a compact camera module by securing an incident angle margin, and a manufacturing method thereof are provided. The unit pixel of an image sensor includes: a first wafer including a photodiode containing impurities having an impurity type opposite to that of a semiconductor material and a pad for transmitting photoelectric charge of the photodiode to outside; a second wafer including a pixel array region in which transistors except the photodiode are arranged regularly, a peripheral circuit region having an image sensor structure except the pixel array, and a pad for connecting pixels with one another; and a connecting means connecting the pad of the first wafer and the pad of the second wafer.