The invention discloses a semiconductor device and a manufacturing method thereof and belongs to the semiconductor technical field. The method includes the following steps that: a semiconductor structure is provided, wherein the semiconductor structure includes a substrate and semiconductor fins on the substrate; dummy gate structures are formed on the semiconductor fins; a first dielectric layeris formed on the semiconductor structure after the dummy gate structures are formed, and the first dielectric layer protrudes out from the upper surfaces of the dummy gate structures; the dummy gate structures and portions of the semiconductor fins covered by the dummy gate structures are removed, so that grooves can be formed, wherein the semiconductor fin is divided into a first portion and a second portion separated from each other through the corresponding groove; and a second dielectric layer is formed on the semiconductor structure after the grooves are formed, wherein the second dielectric layer fills the grooves. With the manufacturing method of the present invention adopted, a non-recessed groove isolation structure can be formed.