The invention relates to a measurement system and measurement method for stress waves of Hopkinson bars by using a flexoelectric effect. The system comprises a bullet, a laser velocimeter, an input bar, an output bar, an absorbing bar, a damper, a first strain gradient sensor, a second strain gradient sensor, a speed measuring circuit and a two-way charge amplifier, wherein the first strain gradient sensor and the second strain gradient sensor are respectively attached to the input bar and the output bar, the speed measuring circuit is optically connected with the laser velocimeter, and the two-way charge amplifier is electrically connected with the first strain gradient sensor and the second strain gradient sensor; the speed measuring circuit and the output end of the two-way charge amplifier are electrically connected with signal processing, displaying and storing modules. During stress wave measurement, a test piece is fixed between the input bar and the output bar, the absorbing bar and the damper are sequentially arranged behind the output bar, and the bullet and the input bar are respectively arranged on the same horizontal plane on the two ends of the laser velocimeter. As the passive strain gradient sensors based on a flexoelectric principle are arranged, the measurement system can measure the first-order derivative of a real waveform, can directly carry out integral computation for the waveform, and can obtain the more real waveform of the stress waves, and the measurement precision is improved.