In this study theoretical investigations were carried out to determine design and working parameters modifications in order to increase by 20% power output and reduce fuel consumption in a marine two stroke medium speed diesel engine with opposite pistons. To achieve the above aim software packages, such as DIESEL-RK, INJECT and ANSYS, were deployed.The phenomenological multi-zone fuel spray combustion model in DIESEL RK software was refined to take into account complex interactions of fuel sprays and the influence of air swirl in the cylinder on evolution of fuel spays. For this purposes a 3D grid was created with regular cubical cells in the combustion chamber of the engine. The density of mesh was 50 cells across the diameter of the cylinder. In contrast to CFD technique, the transfer of liquid fuel and fuel vapour in the computational grid was carried out using empirical equations which had been validated by other researchers. Such novel approach made it possible to preserve the high speed computational performance of DIESEL-RK and good accuracy of modeling. In this new methodology for calculation of combustion in multiple zones only energy balance equation is solved to calculate the temperature of combustion gases, fuel droplets and process of fuel evaporation. Computational time for modeling of one mode of engine's operation takes only few minutes even for the case when 8 side injectors are deployed in the cylinder. For optimisation of angles of sprays orientation a sub-programme is developed in C++ for 3D visualisation of modelling results using the cross platform library OpenGL. With refined model of combustion DIESEL-RK was further developed to make it possible to simulate simultaneous application of several separate fuel injection systems even with supply of different types of fuel into the cylinder. Optimisation of the engine also results in specification of requirements to fuel supply systems. Using such technical specification of requirements and using INJECT software the main design features of the main elements of the high pressure pump, pipe work of the fuel supply system and fuel injector are defined. It was found that the fuel injection pressure should be higher than 2000 bar but lower than 2800 bar so the Common Rail fuel supply system does not have advantages over conventional unit pump systems if no ultra-low limits on the level of emissions are imposed. Finally, the thermal loading of the engine's piston was evaluated using ANSYS software. It was found that the maximum temperature on edges of the piston's crown made of cast iron limits the level of enhancing of engine's performance.