A semiconductor device and a manufacturing method thereof are disclosed. In the device, the isolation layer is used to prevent the first metal layer and the second metal layer which are over-etched and back-splashed from diffusing to a first substrate; and the isolation layer serves as a barrier layer to prevent an interconnection layer from diffusing into the first substrate. Further, the isolation layer includes a silicon nitride layer, which is advantageous for preventing the metal layers from back-splashing and diffusing to the sidewall of the first substrate. The isolation layer further includes a first silicon oxide layer and a second silicon oxide layer, wherein the second silicon oxide layer is used to protect the silicon nitride layer from being etched and consumed and the first silicon oxide layer is used to improve the adhesion between the silicon nitride layer and the first substrate.