The coherence of the fuel injection quantity determines the working stability of the common rail system. The variations in the parameters of the common rail injector have significant influence on coherence of the fuel injection quantity of the system. The bond graphs for the main components of the common rail injector were proposed, respectively, based on the bond graph methodology in this article. The fuel injection quantities of the system at different rail pressures and injection pulse widths had been obtained by numerically solving and programming the obtained state equations in MATLAB. The predicted results of the fuel injection quantity by the model are in excellent agreement with the experimental measurements which were obtained from a test bench. Through the correlation analysis of the influential factors on the fuel injection quantity, the correlation coefficients between the fuel injection quantity and the single influential factor and quadratic influential factor at different rail pressures and injection pulse widths were obtained, respectively. Moreover, the variation characteristics of correlation between the fuel injection quantity and its influential factors had been analyzed in detail. The results show that the nozzle hole diameter and the inlet orifice diameter are the main influential factors on the fuel injection quantity among the selected parameters. The quadratic factors under the action of the parameter itself and the quadratic factors under the interaction between the delivery chamber diameter and nozzle hole diameter, needle seat semi-angle and needle cone semi-angle, nozzle hole diameter and inlet orifice diameter and inlet orifice diameter and outlet orifice diameter have significant effect on the fuel injection quantity, and they are the main influential factors on the fuel injection quantity among the quadratic factors.