Common rail system is a key technology of energy saving and emission reduction for modern diesel engines. Multiple injection, as one of the most interesting features of common rail system, allows both optimal fuel consumption and exhaust emissions. In order to explore the method for controlling the fluctuation of fuel injection quantity during multiple injection, experiments have been carried out in this paper, focusing on pilot-main injection. The high pressure fuel circuits of the system have been equivalent to a spring-mass vibration system. Comparison with the experiment shows that the proposed fluctuation equation can reasonably predict the fluctuation characteristics of main injection quantity with pilot-main injection interval. The correction control strategy for the main injection quantity fluctuation has been proposed, in which the relative damping coefficient, rail pressure, pilot-main injection interval and main injection pulse width are chosen as the input variables. The experimental results with different rail pressure and main injection quantity show that the fluctuation of injection quantity during pilot-main injection can be controlled effectively by the proposed correction strategy. The maximum average fluctuation of main injection quantity decreases by as much as 44.66 %.