To investigate the runoff of bioretention, a rainfall-runoff relationship experiment was conducted. HYDRUS-1D model was applied to simulate the runoff generation processes with different designed precipitation frequency and filter media. The simulated runoff process and ponding duration were in good consistence with the measured data. The results show that the model is able to capture the runoff processes reasonably well of bioretention after parameter calibrated and model validation. With designed precipitation frequency changed from P=100% to P=1% as the rainfall depth from 48.1mm to 423.4mm in 24 hours, the infiltration depth to total flow changed from 90.7% to 25.8% for bioretention with traditional filter media, while it changed from 88.9% to 64.7% for bioretention with large particle filter media. The simulated results indicate that the infiltration capability of bioretention with large particle filter media is better than with traditional filter media, and reducing the amount of outflow and ponding time obviously. However, the delay period with traditional filter media is longer than with large particle filter media. Also the peak flow reduction of the bioretention with traditional filter media is larger than large particle filter media before over flood occurrence.