The Eddy Current Damper (ECD) is a velocity-based passive energy dissipation device that can be used for structural vibration control. This study aims to reveal the damper behavior and determine the optimal parameters of the ECDs applied to a suspension bridge suffering from bi-directional earthquakes. The influence of the bi-directional vibration interaction on the damping force is theoretically investigated. An optimization method is proposed combining the Sobol Sequence sampling method, the Coefficient of Variation (COV) method, and the Backpropagation neural network (BPNN) algorithm. A numerical model of a long-span suspension bridge with bi-directional ECDs is established and taken as a case study to verify the feasibility of the proposed optimization method. The results indicate that the ECD system with bi-directional interaction will produce a larger maximum force and less energy dissipation than one without bi-directional interaction. The proposed optimization method possesses the characteristics of objectivity, accuracy, and effectiveness. The obtained optimal bi-directional ECDs can significantly reduce the longitudinal and transverse vibration. Failing to consider bi-directional effects will lead to an overestimation of longitudinal damper parameters and an underestimation to transverse ones, as well as ignoring the influence of damper length on its mechanical performance.