A multilayer three-dimensional circuit structure and a manufacturing method thereof are provided in the present invention. The manufacturing method includes following steps. First, a three-dimensional insulating structure is provided. A first three-dimensional circuit structure is then formed on a surface of the three-dimensional insulating structure. Next, an insulating layer covering the first three-dimensional circuit structure is formed. Thereafter, a second three-dimensional circuit structure is formed on the insulating layer. Subsequently, at least a conductive via penetrating the insulating layer is formed for electrically connecting the second three-dimensional circuit structure and the first three-dimensional circuit structure.