A micro electronic mechanical system structure and a manufacturing method thereof are provided. A substrate has a plurality of conductive regions is provided. A dielectric layer is formed on the substrate. A plurality of openings and recesses are formed in the dielectric layer, wherein the openings expose the conductive regions. The recesses are located between the openings. A conductive layer is formed on the dielectric layer and the openings and the recesses are filled with the conductive layer. The conductive layer is patterned to form a plurality of strips of the first conductive patterns on the dielectric layer and a second conductive pattern on the sidewall and the bottom of each recess, wherein the first conductive patterns are connected with each other through the second conductive patterns. The dielectric layer is removed. The second conductive patterns between the first conductive patterns are removed.