The present invention relates to a thermally enhanced interconnect substrate and a method of making the same. In accordance with one preferred embodiment, the method includes: forming a stopper on a metal layer of a laminate substrate; removing a selected portion of the metal layer to form a paddle layer; mounting a semiconductor device on the paddle layer using the stopper as a placement guide for the semiconductor device; attaching a stiffener to the laminate substrate; forming first and second build-up circuitries that cover the semiconductor device, the paddle layer and the stiffener at both sides; and providing a plated through-hole that provides an electrical connection between the first and second build-up circuitries. Accordingly, the paddle layer can provide excellent heat spreading, and the stopper can accurately confine the placement location of the semiconductor device and avoid the electrical connection failure between the semiconductor device and the build-up circuitry.