The invention belongs to the technical field of polycrystalline silicon production and in particular relates to a polycrystalline silicon core welding system and a using method thereof. The polycrystalline silicon core welding system comprises a funnel (1) with a funnel neck (3), a heating coil (2), a gas nozzle (7) and a plurality of clampers (8); the heating coil (2) is arranged at the peripheryof the lower part of the funnel (1); the gas nozzle (7) is arranged below the funnel neck (3); the clampers (8) are arranged between the funnel (1) and the gas nozzle (7), are respectively connectedwith a transmission mechanism and are capable of moving in axial and radial directions; and the welding system is arranged in a clean environment. The polycrystalline silicon core welding system has the advantages that the structure is simple and easy to achieve; a silicon core is reliable in welding and high in welding efficiency; the welded silicon core is pollution-free and straight; a weldinghead is flat; and a fractured or/and length-insufficient silicon core is reutilized, the cutting efficiency is increased, and the production cost is reduced.