One of the main issues in the design, modeling, and control of innovative automotive engines is to reduce energy consumption and emission of pollutants and, at the same time, to guarantee a high level of performance indices. In particular, enhanced model-based control of the injection process has been a hot research topic in recent years to increase the combustion efficiency in common rail (CR) diesel engines and to meet strict legislations. This paper focuses on the development of a more accurate model for the electro-injector in CR diesel engines. The model takes into account the mechanical deformation of relevant parts of the electro-injector and the nonlinear fuel flow. Model parameters are then optimized by an evolutionary strategy. Simulation results confirm that the optimized model can be helpful for predicting the real trend of the injected fuel flow rate, evidenced by experimental data, thus can be helpful for injection control of CR diesel engines.