Separation efficiency of eddy current separation (ECS) is low (about 85%) in industrial application for recovering aluminum from crushed waste toner cartridges. Influencing factors of ECS were studied to improve the separation efficiency. Operation factors were researched by orthogonal experiment of ECS on investigating the separation distance between aluminum and plastic flakes. The results indicated the difference (ωR-v) between feeding speed (v) and rotation speed (ω) of magnetic drum (radius: R) was critical factor of influencing the separation efficiency, feeding speed (v) was general factor, and collecting position (H) was subordinate factor. Separation efficiency decreased as the increasing of v, and increased as the increasing of (ωR-v). 0.9 m was the optimal value of H in the orthogonal experiment. Influencing factors of particle characteristics and machine structure were studied by newly established models for computing the separation distance between aluminum and plastic flake in ECS. The results indicated changing of particle size would influence the separation efficiency greater than ω and particle shape. Separation efficiency will increase as the increasing of particle size and ω. Shape of circle is beneficial to improve separation efficiency. Finally, approaches to improve separation efficiency of ECS were presented.