A heat sink structure and a manufacturing method thereof. The heat sink includes a main body and multiple radiating fins each having a folded root section. The main body has multiple connection channels formed on a circumference of the main body. 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 folded root sections of the radiating fins are relatively high-speed thrust into the connection channels of the main body to tightly integrally connect with the main body.