The main challenge for predictive simulation of carbonate reservoirs is associated with large uncertainties in the geological characterization of the reservoir with multiple features including fractures and cavities. This type of reservoirs requires robust and efficient forward-simulation capabilities to apply data assimilation or optimization technique under uncertainties. The interaction between reservoir matrix and various features introduces a complex multi-scale flow response driven by global boundary conditions. The Discrete Fracture Models (DFM), which represent fractures explicitly, is capable to accurately depict all important features of flow behavior. However, these models are constrained by many degrees of freedom and corresponding computational efficiency when the fracture network becomes complicated. The Embedded DFM, which represents the interaction between matrix and fractures analytically, is an efficient approximation. However, it cannot accurately reproduce the effect of local flow conditions, especially when the secondary fractures are present. In this study, we applied a numerical upscaling of DFM models to a triple continuum model where large features are represented explicitly using the numerical EDFM and small features are upscaled as a third continuum. In this approach, we discretize the original geo-model with unstructured grid based on DFM and associate the mesh geometry with large features in the model. Using the global solution, we generate local boundary conditions for the model capturing the response of primary features to the flow. Applying local boundary conditions, we resolve all secondary features using a fine scale solution and update the local boundary conditions. This procedure is applied iteratively using the local-global-upscaling formalism. To demonstrate the accuracy of the Multi-Level Discrete Fracture Model, several realistic cases have been tested. By comparing with fine scale DFM solution and the traditional EDFM technique, we demonstrate that the proposed model is accurate enough to capture the flow behavior in complex fractured systems with advanced computational efficiency.