A method for forming an end surface of a heat pipe and the structure thereof are disclosed. Firstly, the mold module is provided for placing the heat pipe therein. The mold module includes a mold chamber to receive the heat pipe. Then, an extruding shaft is pushed forward into the mold chamber from an end of the mold module. Next, the ends of the heat pipe are compressed via the extruding shaft to render the end surface of the heat pipe depressed from outside to inside. Thereby, the heat pipe with a non-protrudent end surface is obtained. As such, the volume occupied by the useless segment of the heat pipe is effectively reduced, or, the heat pipe having a certain length to cooperate with more heat dissipating fins.