Fractured vuggy reservoir is a typical type of carbonate reservoir. The 3D complex fracture networks and Stokes flow inside vugs make fractured vuggy reservoir simulation remain a challenging problem. Most of the proposed models in previous studies are computation consuming, which cannot meet with the demand of field application. In this paper, a novel and efficient hybrid model, consisting of a modified embedded discrete fracture model (EDFM) and a vug model, is proposed to simulate multiphase flow in 3D complex fractured vuggy reservoirs. The modified EDFM improves the fracture‐discretization process by using two sets of independent grids for matrix and fracture systems, which promotes the modeling of 3D complex fractures in real geological structures. Meanwhile, the vug model simplifies the coupled porous‐free flow with the assumption of multiphase instantaneous gravity differentiation. The accuracy of the modified EDFM and the vug model is demonstrated by comparing the results with those of the conventional EDFM and volume of fluid (VOF) method. After that, a series of case studies, including three conceptual fracture‐vug unit models and a real field model, have been conducted to test the proposed hybrid model. The results of the three fracture‐vug unit models indicate the significant effect of a local fracture‐vug structure on the flow characteristics and production performance. Finally, the application with a real field model with 3D complex fracture and vug geometries further verifies the practicability of our proposed model in real fractured vuggy reservoirs.