The invention provides a Schottky barrier diode device structure and a manufacturing method of the structure. The device structure comprises a first conductive type substrate, first conductive type epitaxial layers which are combined on the surface of the first conductive type substrate, a plurality of groove structures, second conductive type doping areas, a Schottky metal layer and an upper electrode. The groove structures comprise grooves formed in the first conductive type epitaxial layers, dielectric layers combined on the surfaces of the grooves, and conductive materials, the grooves are filled with the conductive materials, the second conductive type doping areas are formed at the positions, arranged on two sides of the groove structures, of the surfaces of the first conductive type epitaxial layers, and the Schottky metal layer is formed on the surfaces of the first conductive type epitaxial layers. The doping areas are added on two sides of the groove structures, the P / N knot is introduced, electric fields of the areas are reduced, and therefore reverse leakage currents are reduced. Meanwhile, JFET structures are introduced between the doping areas, reverse breakdown voltages of the Schottky barrier diode device structure are improved, and the reverse leakage currents are reduced.