This paper proposed a real-time simulation model of a diesel engine based on the fuel transfer in the combustion zone and an array calculation method. The proposed model conducts real-time optimized modelling of the diesel engine multi-zone model from two aspects: a modelling method and a model algorithm. From the modelling method perspective, the model proposed a combustion process model that transfers fuel mass and momentum between the combustion zones. Based on the diesel combustion characteristics, this modelling method divides the cylinder into three thermodynamic zones: an unburned area, a premixed combustion zone, and a diffusion combustion zone. This division addresses the assumption that fuel mass and momentum transfer are not performed between Combustion zones in the traditional multi-zone model. While reducing the computation regions and improving the simulation calculation speed, the combustion process of the premixed combustion zone and the diffusion combustion zone were described using the method of Stefan flow and entrainment combustion. The physical depth and the predictivity of the model was enhanced, which rendered the description of the combustion process more consistent with the diesel combustion characteristics. The thermodynamic calculation process of the three regions was maintained throughout the entire cyclic operation in the entire diesel engine operating cycle. From the model calculation perspective, the model proposed a direct single-step calculation method for temperature and pressure to satisfy the demand of real-time model calculation. To optimize the multi-cylinder multi-zone plan in a real-time environment, the model utilizes an array method for calculation. The results of the model verification of a diesel engine in high and low loading conditions and using fixed combustion model parameters indicate that the difference between the calculation results and the experimental data is less than 5% and the results are consistent, which proves that the model has predictivity. The analysis of the model calculation results indicates that the model can accurately reflect the performance change pattern and regional change characteristics for different working conditions and provide a suitable foundation platform for controlling system combustion performance optimization. In addition, the array algorithm and multi-zone through-operation calculation method were validated in a real-time hardware system test environment. The methods can effectively reduce the multi cylinder multi-zone model simulation time to 30%. The application range of the real-time system model was expanded; thus, this method is very suitable for real-time system calculation.