Abstract: The injection process of electron storage ring is a special transient process. The mismatch between the injector and the storage ring can be evaluated online by studying the 3D merging of refilled charge and stored charge. For the next-generation light source, it can lay a technical foundation for building a diagnostic system. The beam instrumentation group of the Shanghai Synchrotron Radiation Facility developed a 3D bunch-by-bunch diagnostic system based on button pick-up signal and high-speed acquisition boards to measure the beam transverse position and longitudinal phase. Extracting the 3D position information of the refilled charge during the injection process is the critical issue in this system. The charge-weighted average method was proposed to extract the transverse position and the proportional coefficient method was proposed to extract the longitudinal phase. The transverse betatron oscillation and longitudinal synchrotron oscillation of the refilled charge were analyzed. 3D position information of the refilled charge and several dynamic parameters of ring, such as longitudinal maximum oscillation amplitude, initial arrival time and synchrotron damping time, can be extracted during the user operation mode, which provides a strong toolkit for accelerator physics.