A three-layer TOPMODEL is constructed by integrating diffusion wave approach into surface flow, soil moisture deficit into inter flow and exponential recession curve function into base flow. A subtropical mountainous watershed, Heng-Chi, and 22 rain storms with various rainfall types and wide ranges of total rainfall (from 81 to 1026 mm) were applied. The global best-fitted parameter set gives an average efficient coefficient of 82% for calibration and 80% for validation. Sensitivity analysis reveals that soil transmissivity dominates the discharge volume and recession coefficient dominates the hydrograph shape in TOPMODEL framework. Over 90% observed discharges of validation events falls within the 90% confidence interval derived form calibration events. The resembling performances between calibration and validation as well as good results of the confidence interval demonstrate the capability of 3-layer TOPMODEL on simulating cyclones with various rainfall intensity and pattern in subtropical watershed. Meanwhile, the upper confidence limit is suggested preferably when considering flood assessment.