In this study, the ecological flow rate of the Zacco playtypus habitat was simulated based on the Instream Flow Incremental Methodology (IFIM) in reachs of urban and natural stream using the habitat suitability index (HSI) of the probability density function (PDF). To apply this method, PHABSIM model was used in this study. However, in this study, the HSI of the probability density function was developed by adjusting the parameters of the PDF based on Kang (2010) HSI. As a result, the normal distribution is closest to the ecological flow rate of the Kang (2010) in the urban stream. However, the two-parameter log-pearson distribution tended to be the closest in the natural stream. The ecological flow rate was simulated by the HSI and the reach of stream with the PDF. Based on the comparison of simulation results, we propose an ecological flow rate estimation method using probabilistic method.