Introduction: Today, maximizing the efficiency of fuels and increasing the output POWER of diesel engines is considered inevitable due to the increasing need for energy resources, the reduction of fossil fuel resources, the need to maintain the environment, reduce air pollution, and limit the electricity supply and fuel supply. In the large cities of Iran, the problem of vehicle pollution is one of the main problems. The lack of proper fuel, soot filters, and absence of requirement for a technical inspection of diesel vehicles have led to an increase in mortality and the growth of lung cancer due to pollution. All of studies indicate that fossil fuels, despite the low cost of production, will increase the cost of both living and environment. A solution for this crisis is to reduce the sources of pollutant-producing sources from the source of these pollutants. In the internal combustion engines, the compression ratio and alternative fuels are two important factors affecting engine performance and exhaust emission. Materials and Methods: In this research, a one-dimensional computational fluid dynamics solution with GT-POWER software was used to simulate a six-cylinder diesel engine to study the performance and exhaust emissions with different compression ratios and alternative fuels. The compression ratio was chosen to be 15: 1 to 19: 1 with an interval at unity. Alternative fuels such as (as base diesel), methanol, ethanol, diesel and ethanol, biodiesel and decane were selected. To modeling engine, first, all parts of the engine were introduced as a real six-cylinder engine, and then the required data were entered according to the actual engine conditions at the atmospheric pressure of one atmosphere. Before this investigation was carried out, a validation model for evaluation was done by experimental and simulation data. The validation results showed that software model error is acceptable and the model has a good capability of fitting and predicting. Results and Discussion: The engine performance was evaluated in terms of engine POWER, engine torque, and specific fuel consumption at different engine compression ratio and fuel. The results showed that with increasing the compression ratio, brake POWER and brake torque increased. Among the fuels used in this engine, the maximum brake POWER and brake torque in the compression ratio of 19 with the decane fuel were 3. 86% higher than that the base fuel and the lowest value was awarded in the compression ratio of 15, with methanol fuel and it was equal with 56. 04%. The results indicated that by increasing compression ratio, the brake specific fuel consumption was reduced due to more POWER than the fuel consumed in the engine. A fuel with lower heating value should be injected more mass to the engine. This will increase the brake specific fuel consumption. In this research, the decane fuel with a compression ratio of 19 with a reduction of 3. 72% had the lowest brake specific fuel consumption among other fuels. The CO emission from the engine largely depended on the fuel's properties, the availability of oxygen, the fuel mix with air, temperature, and turbulence inside the combustion chamber. The results highlighted that by increasing compression ratio, CO emission increased and CO emission in biodiesel fuel, with a compression ratio of 15, was decreased by 82. 37% compared to the base. CO2 emissions are not too harmful to humans, but they increase the potential for ozone depletion and global warming. With increasing compression ratio, CO2 and HC emissions increased for all fuels, CO2 emissions have risen up the base. The fuel heating mechanism, combustion temperature, oxygen content, and gas fuel availability are the most important factors in the formation of NOx. With increasing the compression ratio, the amount of NOX increases, which is due to the high temperature in the cylinder at a higher compression ratio. The viscosity and density of fuels have an effect on NOX emission, and because of the larger droplets of the fuel, it released NOX. The highest NOx emissions from biodiesel fuel are due to the high oxygen content of this fuel and the lowest NOx emissions from decane fuel, due to the low density of the fuel compared to other fuels. Conclusions: The results of this study showed that the decane fuel with a compression ratio of 19 in total had the best functional and pollutant characteristics among the six fuel used in this study. Therefore, this fuel can be the best alternative for diesel fuel.