A heat sink structure and a manufacturing method thereof. The heat sink includes a main body having multiple main body connection sections and multiple radiating fins each having a connection section. The main body has a first end and a second end. The first and second ends define a longitudinal direction. The multiple radiating fins are placed in a mold. A mechanical processing measure is used to high-speed impact the main body so as to thrust the main body into the mold. Accordingly, the connection sections of the radiating fins placed in the mold are high-speed thrust into the main body connection sections and moved in the longitudinal direction to the second end of the main body to tightly integrally connect with the main body.