The article presents the results of developing software for calculation and optimization of diesel operating processes and fuel injection. The software is intended for calculation and optimization of operating processes and fuel injection for supercharged and naturally aspirated diesel engines, including those running on alternative and mixed fuels, with a multi-phase injection and exhaust gas recirculation, at the start mode and partial loads. The software consists of related modules: user interface for data input, running control and calculation results display, data exchange between modules, a module for one-dimensional calculation of processes in the common rail fuel systems, a module for thermodynamic calculation of operational processes and conjugate calculation of the thermal state of combustion chamber parts using finite element method, a module for three-dimensional calculation and optimization of operations in the combustion chamber using computational fluid dynamic (CFD) method. A distinctive feature of the software is a conjugate calculation of fuel injection, operational processes, and thermal state of the combustion chamber parts. The use of this software can significantly reduce the time required to optimize operational processes, solve problems of engine forcing, reduce fuel consumption and reduce emission rates.