Injection rate shaping is one of the key measures to achieve energy saving and emission reduction in diesel engines. To apply this technology to marine low-speed engines, an innovative Boot-Electronically Controlled Injector (Boot-ECI) has been proposed. This new type of injector, featuring innovative injection rate shaping technology, effectively compensates for the shortcomings of traditional methods in terms of economic efficiency and operational stability, making it particularly suitable for application in marine low-speed engines. Based on the established models of the injector and a single-cylinder low-speed engine, this study thoroughly investigates the impact of switching delay time (tsd) and strat of injection (SOI) of the Boot-ECI on the indicated specific fuel consumption (ISFC) and NOx emissions of the engine. Through comparative analysis, the study reveals the differences in the roles of Boot-ECI and Traditional Electronically Controlled Injector (TECI) during the combustion process in engine and further discusses the specific impact of low lift of the Boot-ECI selection on engine performance. The results indicate that for Boot-ECI, employing a larger tsd offers a more pronounced advantage in reducing NOx concentration per unit increase in ISFC under low-load conditions compared to delaying SOI. When Boot-ECI performs a boot-shaped injection, there is an inflection point in the apparent heat release rate (AHRR) during the rise phase, which is associated with the transition from a low injection rate in state I to a high injection rate in state II during the boot-shaped injection. Compared to TECI, Boot-ECI demonstrates superior performance in managing the trade-off between NOx emissions and ISFC. Furthermore, as the needle low lift of the Boot-ECI increases, the contribution of SOI to NOx concentration reduction per unit increase in ISFC remains constant, while the contribution of tsd increases, especially at 25% load.