A system for tracing and imaging magnetic field configuration of a stellarator, including an electron beam emission and adjusting unit, a dynamic fluorescence imaging unit and an image acquiring unit. The stellarator includes a vacuum chamber and a three-dimensional vacuum magnetic field formed in the vacuum chamber. The electron beam emission and adjusting unit is configured to emit an electron beam. The dynamic fluorescence imaging unit includes a fluorescent grid and a grid drive mechanism. The fluorescent grid is arranged at a Poincaré surface of section located in the three-dimensional vacuum magnetic field. The grid drive mechanism is configured to drive the fluorescent grid to periodically reciprocate. The image acquiring unit is configured to image the fluorescent grid. A method for measuring the magnetic field configuration based on the system is also provided.