The invention discloses a three-level VIENNA rectifier model prediction control system and method under a power grid unbalanced condition. The invention solves problems of the calculation of referencecurrent when the power network is unbalanced; the balance control of dc side voltage and DC side neutral point voltage; three-phase current zero-crossing distortion; control of unit power factor of grid current. The algorithm divides 25 voltage vectors into 6 sectors according to the current direction and 8 voltage vectors in each sector. Then five voltage vectors are selected according to the deviation of the neutral point voltage, and the optimal space voltage vector is obtained according to the value function, and the optimal space voltage vector controls the state of the switch transistor, so as to realize the control of the three-phase three-level VIENNA rectifier. The algorithm does not require the separation of positive and negative sequence of voltage and current, phase lock of voltage, current inner loop control module and modulation module when the power network is unbalanced.