A method for manufacturing a heat pipe cooling device. The heat pipe cooling device includes a U-shaped heat pipe, which is embedded within a heat conductor. The heat conductor includes a rectangular base and an upper cover connected to the base. The base includes many retaining grooves which allow the absorption end of the heat pipe to be disposed therein. The upper cover includes many through holes formed thereon corresponding to the cooling end of the heat pipe. The bottom surface includes many protrusive portions corresponding to the inner side of the absorption end of the heat pipe. Furthermore, the upper cover and the base both include a positioning portion for engaging each other. In this manner, the upper cover is pressed on the cooling end of the heat pipe. The protrusive portion will push the heat pipe to tightly contact with the base. Finally, a planarization process is performed, thereby making the bottom surface of the absorption end and the bottom surface of the heat conductor to form a flat surface.