Tpx3Cam is a newly developed time-stamped camera. With the ability to record the arrival time and position of each event simultaneously, it becomes a powerful tool in atomic and molecular research. As an inherent weakness, the time-walk effect resulting in a deviation in the arrival time is a major obstacle in improving the experimental resolution and reconstruction of momentum along the time-of-flight. We developed an analytic expression to describe and correct the time-walk effect, which is independent of different fragments once the parameters of the spectrometer, the microchannel plate (MCP), the phosphor screen, and the Tpx3Cam, such as voltages on the spectrometer and MCP, are fixed. With the time-walk correction, 3D momentum distributions of N+ and N2+ from the N2 molecule’s Coulomb explosion were well extracted, paving a way for filming molecular dynamics in three dimensions with time-stamped velocity map imaging. Simultaneously, a denoising method based on data filtering is presented for Tpx3Cam.