Urban flooding is a big problem for developing countries like China. The parameterization of urban water balance schemes is important to urban latent heat flux and urban land-atmosphere interaction studies. Now, various kinds of urban hydrological schemes are developed to simulate the urban water cycle; but some key physical processes about urban water balance still need to be addressed. In this paper, the urban water balance schemes are developed and coupled with the Integrated Urban land Model (IUM) to improve the urban modelling framework. The inundation depths on natural, urban road and urban roof surfaces are used as prognostic variables of water balance equations. The results indicate the values of urban latent heat flux are associated with the duration time of water inundation. After parameter calibration based on the observed inundation depths in road sites, IUM can simulate water inundation depths well compared to those of the observations. Based on mechanism study, several mitigation strategies were put forward and sensitivity analyses were implemented. The results indicate these mitigation strategies can reduce the urban inundation depth and shorten the inundation duration time.