Start of fuel injection and fuel type are two important factors affecting engine performance and exhaust emissions in internal combustion engines. In the present study, 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 injection timing and alternative fuels. Starting the fuel injection from 10 °CA BTDC to the TDC with an interval between two units and from alternative fuel bases (diesel), including methanol, ethanol, diesel and ethanol compounds, biodiesel and decane. To validate the model, a comparison was made between simulation data and experimental data (including torque and power), which showed that the validation error was less than 6.12%, which indicates the software model validation. Also, the modeling results showed that decane fuel had a higher brake power and brake torque of more than 6.10 % while fuel injected at 10 °CA BTDC compared to the base fuel, and illustrated a reduction of 5.75 % in specific fuel consumption due to producing higher power. In addition, with the advanced of injection timing compared to baseline, the amount of CO and HC in biodiesel fuel reduced and it’s amount was 83.88% and 64.87% respectively, and the lowest NOX emission with the retardation of starting injection, to decane fuel was awarded. In general, the results showed that decane fuel could be a good alternative to diesel fuel in diesel engines when it started fuel injection at 10 °CA BTDC.