The eddy current separator is the key equipment used for the separation and enrichment of non-ferrous metals from the solid waste. The customization and universality requirements for eddy current separators have been improved with the increasingly strict environmental protection requirements in various industries and the pursuit of higher economic benefits by enterprises. The low separation efficiency of the small-sized non-ferrous metals and the difficulty in separating between non-ferrous metals are two urgent problems that limit the development of the eddy current separation. The separator structures design, the factors regulation and the core component magnetic roller optimization are the keys to solve problems. Vertical and horizontal eddy current separators are the two main types of permanent magnet eddy current separators in practical applications and reported studies. However, the study and production cost of the eddy current separator are high, and there are few reports on the separator structures in existing studies. There is also a lack of comparative analysis of different applicable conditions for eddy current separators and optimization design of the magnetic roller. This study compared and analyzed the effects of different factors on the vertical and horizontal eddy current separation efficiency, and clarified the advantages and prospects of the vertical eddy current separator in optimizing the separation efficiency between non-ferrous metals. The comparison and multi-objective optimization were conducted on the magnetic rollers to expand the particle size range that can be separated. The separation performance and the economy of the magnetic roller have been improved significantly, and the performance indicators are better than those of existing equipment with the same specifications. The magnetic roller with specific structural parameters has increased eddy current force and magnetic efficiency density by 75.0% and 63.5%, respectively. It is expected to further expand the applicable materials for the eddy current separator.