Eddy current damper (ECD) is a promising device for dissipating kinetic energy in dynamic systems, this study is conducted to analyze the dynamic characterization and structural optimization of linear ECD under guns launch load. The recoil resistance of ECD under guns launch load is highly nonlinear at high recoil velocity, and the recoil resistance curve shows an increase-decrease-increasing shape like a “saddle”, which is not conducive to the stability of ECD during operation. The effects of several structural parameters on the dynamic characterization of ECD were studied in details. Results show that the air-gap size, the thickness of the magnetic conduction tube and conductive tube all have a notable influence on the recoil resistance curve of ECD. Moreover, BP neural network and genetic algorithm were used for structural optimization and the optimal value was verified by FEM. The optimization results indicate that the “saddle” shape of optimized recoil resistance curve is basically invisible. The fullness of the recoil resistance curve is significantly improved from 84.93% to 92.1%, which guaranteeing a smooth recoil movement. Finally, an impact loading test system for eddy current damper was built and the experimental results were basically consistent with the simulation results.