With the accelerated urbanization process, cities are suffering from extremely heavy rain and urban storm water logging disasters in recent years. To provide reliable and effective information for urban management and emergency decision-making, the accuracy of basic data must be guaranteed in any urban rainwater model. This paper presents a novel MKFCM-MRF (Multiple Kernel Fuzzy C Means-Markov Random Field) model to segment high-resolution Unmanned Aerial Vehicle (UAV) images. The core ideas of MKFCM-MRF model are as follows. Firstly, in order to increase the correlation information between pixels, multiple-kernel functions are introduced into Fuzzy C Means (FCM) clustering algorithm, which automatically filters out the optimal weight combination among kernel functions according to the distribution characteristics of pixels in feature space. Secondly, in order to better segment the texture and edge of the image, the clustering results of multiple-kernel FCM clustering algorithm are introduced into Markov Random Field (MRF) model, a novel spatial energy function integrating fuzzy local information is constructed. Finally, based on the total of data and spatial energies, the raw clustering results are regularized by a global minimization of the energy function using its iterated conditional modes (ICM). The effectiveness of MKFCM-MRF is performed by high-resolution UAV images data. The experimental results indicate MKFCM-MRF can refine the classification map in homogeneous areas, while reducing most of the edge blurring artifact, and improving the classification accuracy compared with FCM clustering algorithm. In addition, the validation of the urban storm flood model shows that the trend of the two clustering results is the same, but the runoff producing time and the peak time of FCM clustering results are advanced, the peak flow and the total runoff are larger; the simulation results corresponding to MKFCM-MRF clustering results are more realistic.