Fuel spray characteristics is known to significantly affect the combustion and emission processes in diesel engines. High-pressure common-rail system can supply so high injection pressure for getting the better spray characteristics to enhance combustion efficiency and reduce emission. With the fuel injection pressure increasing, spray process becomes more and more complex which makes the study on atomization mechanism more challenging. Under the super high injection pressure, the internal turbulent flow and cavitating flow of the nozzle will greatly influence the subsequent fuel atomization process and spray characteristics, especially the cavitation has been the key to relating internal flow of nozzle and atomization behavior. So it is necessary to simulate the fuel spray process considering of internal cavitating flow of the nozzle. In this paper, firstly, the high-precision three-dimension structure of nozzle with detailed internal geometry information were obtained using synchrotron radiation x-ray phase contrast imaging technology, which was used for the mesh generation of three-dimensional numerical simulation of the cavitating flow in the nozzle. Then the spray model coupled with nozzle cavitating flow was setup in FIRE v2010 and validated by the spray experimental data got from the high-speed imaging technology on a high-pressure common-rail injection system. The spray simulations coupled with cavitating flow showed that the cavitating flow characteristics in nozzles have a large effect on both macroscopic properties and microscopic properties. Finally basing on the above verified spray model, multi-scheme simulations with various geometry parameters of nozzle were performed and the effect of nozzle geometries on the spray characteristics was analyzed and it was concluded that the nozzle sac volume, hole inlet curvature, hole inclination angle, injector needle lift and needle eccentricity had obvious effects on the nozzle flow and subsequent spray, and there was an opposite trend between the spray penetration and Sauter mean diameter, which provided a certain reference value for structure optimization of the fuel system.