As a state-of-the-art injection technology, high-pressure common rail injection system (HPCRIS) has advantages including high injection pressure, adjustable injection timing and flexible injection rate. Nevertheless, the fluctuation of cyclic fuel injection mass (CFIM) in HPCRIS with multiple-injection strategy (MIS) reduces the economy of diesel engine and the stability of vibration and noise control. To realize the precise control of CFIM, the online perception of injection process is the premise. This paper presents an innovative online measurement method of injection rate on MIS. According to the evolution characteristics of water hammer pressure oscillation in the fuel system, the rule is found that the oscillation form of the water hammer is depended on the structure of HPCRIS rather than the injection condition, and the general applicability of this rule is proved by the hydraulic-electric analog method. Base on this, the real-time simulation method of the pilot water hammer oscillation wave in the same field is proposed to realize the extraction of the expansion pressure signal components of the main injection. Then the direct mathematical relationship between pressure signal and fuel injection rate is established, and the online measurement of fuel injection characteristics under MIS is realized. To improve the robustness of the algorithm a real-time calibration method of fuel sound velocity is proposed. Finally, by comparing with the offline experiment, this online measurement method of injection rate has relatively high accuracy, the CFIM error is less than 2%, and the fitting goodness of the injection rate curve exceeded 0.91. This measurement method can provide direct feedback to the electronic control unit (ECU) on the fuel injection process without changing the HPCRIS structure.