Simulation investigations of flow characteristic in diesel nozzles are basically performed using the simplified and idealized geometry models. Therefore, these simulations are essentially two-dimensional (2D), and unavoidably have deviations from real flow characteristics due to lack of three-dimensional (3D) geometry information. In this study, based on the high energy x-ray CT scan, the inner nozzle structures are measured in detail, and the measurement results are applied to generate the 3D computational meshes. The results of the 2D and the 3D simulations are compared to see the effect of the 3D simulation on the flow characteristics in the nozzles. The investigation results show that because of the rough surface and uneven distributions of geometry parameters in the azimuthal direction of the nozzle orifice revealed by the CT scan, the differences of the flow characteristics between the 2D and the 3D simulations are obvious. They exist at the orifice inlet, the orifice outlet, and along the orifice axis. The improvement of evenness of geometry parameter distributions can reduce the differences between the 2D and the 3D simulations. The 3D computational mesh, which contains more geometry parameter information than the 2D one, can reveal details of the influences of geometry parameters on the internal flow of nozzle, and gain more precise simulation results and insight into the flow characteristics under the real nozzle conditions.