A discharge-fluid coupling simulation was carried out in order to investigate the effect of the pulse polarity on discharge process and flow structure induced by a nanosecond-pulse-driven plasma actuator. The result of the discharge simulation shows that the pulse polarity has an impact on the discharge structure and current waveform. The total amount of the deposited energy to the gas is larger in the positive pulse case than in the negative pulse case when the same peak amplitude pulses are applied. The pulse polarity also affects the structure of the induced shock wave; the shock wave consists of planar and circular parts for the positive pulse case, while no planar part is obtained for the negative pulse case. The difference of the shock wave structure is caused by the difference of the discharge structure. Our result suggests that the positive pulse is preferable to heat large area, while the negative pulse is superior in view of the efficient generation of the strong shock wave. The difference of the shock wave structure would affect the performance of the flow separation control.