The invention relates to an over-voltage protection method for a modularized multi-level voltage source commutation valve. The over-voltage protection method for the modularized multi-level voltage source commutation valve comprises the following steps of: 1) determining the harshest fault working condition which causes the over-voltage stress of the modularized multi-level voltage source commutation valve; 2) determining the lightning arrester configuration mode of the modularized multi-level voltage source commutation valve; and 3) selecting a lightening arrester parameter. The step (2) of determining the lightning arrester configuration mode of the modularized multi-level voltage source commutation valve comprises the following sub-steps of: (2.1) determining a centralized protection scheme of the lightning arresters; (2.2) determining the dispersive protection scheme of the lightening arresters; (2.3) determining the amount of the lightening arresters of single convertor station; (2.4) determining the working voltage of the lightening arresters; and (2.5) determining an optimal lightening arrester protection scheme. According to the scheme provided by the invention, the over-voltage level of the voltage source commutation valve is effectively inhibited, the safe and effective operation of the voltage source commutation valve under various working conditions is protected, and the technical economy of the voltage source commutation valve is improved.