Modelling of Naturally Fractured Reservoirs (NFR’s) is a very challenging task. NFR’s are often simulated using the dual-porosity (DP) model, which requires significantly lower computational time and less simulation cost compared with the fine-grid modelling. However, the DP model is unable to capture the transient effect, the saturation front, and its tendency to overestimate the predicted oil recovery, as the invaded fluid is immediately reaching the gridblock centre once its saturation exceeds the critical saturation. The matrix block discretisation and modifying the transfer function are among the widely investigated areas to represent the transient effect and to improve the simulation accuracy. Adjusting the transfer function often results in complicated and unstable solutions, which make this approach limited in use. However, the matrix discretisation technique, such as Multiple Interacting Continua (MINC), is one of the utilised approaches to improve the simulation of NFR’s. The model’s layers provide the required mean to capture the transient effect and to include the matrix heterogeneities. In this work, we present an improvement to the original MINC model to enhance its accuracy and stability using a particular case of two subdomains model. We suggested using an equal volume of the matrix sub-blocks, besides performing an adjustment to the calculation of fluid saturation. The new adjustments have provided a stable solution and improved simulation results compared with the original MINC model. Besides the advantage of the matrix layers to handle various heterogeneities with excellent simulation accuracy and marginal errors, and hence a reliable performance and prediction.