The present invention discloses a voltage reference reconfiguration fault-tolerant control method for a cascaded multi-level inverter. The fault-tolerant method for the inverter automatically reconfigures the three-phase voltage amplitudes and phases of the three-phase total voltage in accordance with the fault diagnosis, thus realizing three-phase voltage balance. On the basis of the reconfiguration of the total voltage signal, re-reconfiguration of reference voltage inputted into the various H-bridges is conducted in accordance with the fault signal vectors, thereby realizing removal of the fault bridges and fault-tolerance of the normal bridges, while guaranteeing the integral sinusoidal characteristics of the actual reference voltage. The inverter realized maximum three-phase balanced line voltage in a fault occurrence, has the advantages of requiring no redundant modules and algorithms and the advantages of ease of removing fault bridges, and is applicable for reduced load operable electrical equipment.