In order to make high pressure common rail system of the marine diesel engine select injection rate in a flexible way, the double-lift electronically controlled injector, whose needle valve has two upper limit positions, was proposed. An AMESim model of the injector was established, and based on the model, injection quantity characteristics and needle displacement, injection rate, pressure of the delivery chamber with different control timing of the injector under different injection modes and rail pressure were investigated. The results show that, the lift of needle valve is capable of being switched under different rail pressure, enabling the injector to realize three basic injection modes of low lift, high lift and boot. Compared with high lift injection mode, the injector under low lift injection mode has higher control accuracy on injection quantity, and the injection quantity changes almost linearly with the IPW. When the injector is in low lift injection mode, the balance point of delivery chamber pressure fluctuation due to the needle opening will be slightly higher than that of high lift injection mode. The variation of average injection rate with rail pressure under low lift injection mode is smaller than that under high lift injection mode, thus the injection rate fluctuation of low lift is less affected by delivery chamber pressure fluctuation. When the injector is in boot injection mode, lift switching delay is used to describe the time lag of lift switching signal to injection signal. As the value of lift switching delay increases, the change of injection quantity with rail pressure and injection pulse widths transits from high lift injection mode to low lift injection mode. The start time of lift switching has significant effects on the fluctuation of delivery chamber pressure and injection rate in the subsequent fuel injection process.