A control system for reducing drive shaft vibration of an environment-friendly vehicle includes: a drive shaft speed extraction unit that extracts an actual drive shaft speed of a motor and extracts a drive shaft speed from which a forced vibration component that is to be transferred by an engine to the drive shaft is removed; a model speed computation unit that calculates a model speed of the drive shaft; a free vibration computation unit that computes a free vibration component on the basis of deviation between the drive shaft speed and the calculated model speed; and a first torque computation unit that calculates, from the free vibration component, a free vibration reduction compensation torque for reducing the drive shaft vibration.