Multiple injections that are necessary to reduce emissions, noise, and vibration of diesel engine have been accomplished by common-rail fuel injection system. Especially a fuel amount of each injection has to be tightly controlled, but actually there is a difference between an actual amount and a target one. Injection period will be determined according to a map in that the relation between injected amount and injection period is stated. But in the case of multiple injections, pressure wave caused by previous injections remain in a common-rail system at the time an injection second or later starts. Therefore, actual amounts injected will be different from target ones. In order to compensate the difference, the method that the influence of pressure wave on fuel amount injected is also investigated and injection period will be corrected is realized in an actual engine control system. Meanwhile, pressure wave propagation in common-rail has been studied. Generally, difference method and finite element model are used for a simulation of hydraulic transient phenomena in pipelines, which gives unrealistic results by errors of natural angular frequencies. In this paper, optimized finite element model (OFEM) that reduces the errors by optimizing division of elements is adopted to common-rail fuel injection system to analyze flow and pressure wave in pipelines. Models of components in common-rail system, such as high pressure pump, common-rail, injectors, and high pressure pipe are made, then rate of injection and pressure propagation were simulated in the cases of single injection and multi injections. The simulation results were accommodated to experimental ones, and it is strongly suggested that fuel injection control in diesel common-rail will be improved by using OFEM.