We developed a continuous water treatment system consisting of an ozone generator, an ejector nozzle, and a pulsed discharge device. We confirmed that the synergistic effect on indigo carmine decomposition by a combination of ozone injection and electrical discharge exists. In this paper, in order to maximize the synergistic effect, we investigated the effect of the number of electrode pairs and injected ozone gas concentration on indigo carmine decomposition. The results obtained are as follows; (1) discharge energy did not change, when we change the number of electrode pairs. However, average power increased with increasing the number of electrode pairs due to the increase in discharge probability. Large number of electrode pairs leads to a positive effect on indigo carmine decomposition, (2) the synergistic effect increased with increasing injected ozone gas concentration, (3) the reduction of ozone bubble size and the increase of the number of ozone bubbles by pulsed discharge generation is not the cause of the increase of synergistic effect, and (4) we confirmed that the amount of OH (309 nm), Hα (656 nm) and O (777 nm) increased with increasing injected ozone gas concentration. This result suggested that the increase of radical generation from the ozone molecule by pulsed discharge is the cause of the increase of synergistic effect.