The invention provides a junction-barrier controlled Schottky diode and a manufacturing method thereof. The junction-barrier controlled Schottky diode comprises an active region composed of N-type semiconductors, and a plurality of P-type doped regions are arranged in the active region and distributed in the active region in a dot matrix structure mode; the distance between any two adjacent P-type doped regions is equal to that between any other two adjacent P-type doped regions so that the P-type doped regions required by the junction-barrier controlled Schottky diode can have the minimum number and the minimum area under the circumstance of the same area of the active region, and namely the so-called dead-zone area is minimum. Compared with distribution of P-type doped regions in the prior art, distribution of the P-type doped regions is beneficial to improving forward conductivity of the junction-barrier controlled Schottky diode.