The invention provides an inverter current compensation control method for a neutral point clamped three-level topological structure. The inverter current compensation control method for the neutral point clamped three-level topological structure comprises the following steps that S1, the load current and the load voltage of each phase are detected; S2, standard sine signals 2sin(omegat-2mpi/3) and 2sinomegat and standard cosine signals 2cos(omega t-2mpi/3) and 2cosomegat according to the load voltage of each phase; S3, the currents obtained in the step S1 and the standard sine signals and the cosine signals obtained in the step S2 are multiplied, filtering is conduced by a low-pass filter with cutoff frequency higher than two times of fundamental frequency, and then the direct-current component of the load current of each phase is obtained; S4, the amplitude value of a compensating current object of the load current of each phase is calculated according to a calculation matrix and the direct-current component, obtained in the step 3, of the load current of each phase; S5, the amplitude value of each compensating current object and the phase of the load current of each phase are multiplied, so that the ideal currents iA, iB and iC of all the phases are obtained; S6, the load currents of all the phases are subtracted from the ideal currents iA, iB and iC of all the phases, so that order signals ia, ib and ic of the compensating currents of all the phases are obtained.