High-voltage pulse can be used in electroporation by applying a pulsed electric field (PEF) to the sample. The shape of the pulse waveform, voltage amplitude, number of pulses, single pulse duration, and frequency are the basic controllable variables required for the application of PEF. In order to meet the requirements of different waveforms for the cell electroporation, a novel bipolar modular multilevel generator is proposed in this article, which is composed of a special full-bridge (FB) module and a number of half-bridge (HB) modules. Compared with other structures, this structure is relatively simple and the control method is flexible. It can greatly reduce the number of semiconductor switches with the same number of output levels. An experimental prototype is built to verify the scheme which can output bipolar nine levels with 12 semiconductor switches. The different required waveforms can be obtained by controlling the timing. Finally, the system achieves the maximum output voltage of ±2 kV, adjustable frequency from 1 to 100 Hz, and a total of 19-level voltage output (including positive levels, negative levels, and 0 level).