The present disclosure provides a vehicle body transfer system using a transfer unit. The system may include a base configured to move along a base rail; a moving unit comprising a supporting part that is configured to support a vehicle body, wherein the moving unit is configured to move the supporting part in a predetermined direction and the moving part is disposed on the base; and a tool unit disposed outside the base rail and selectively engaged to the moving unit, wherein the tool unit is configured to provide a driving torque such that the moving unit controls a position of the supporting part.