High gradient magnetic separation (HGMS) is an effective method to recover fine weakly magnetic particles from a suspension. Magnetic matrices are the crucial components of the HGMS system. The most commonly used matrices in HGMS are cylinder matrices of high magnetic permeability. Special cross-section shape matrix may have better magnetic characteristics and show better performance than circular cross-section matrix in HGMS. The particle capture of elliptic cross-section matrix in the three configurations of HGMS are modeled and investigated, aiming at revealing the application possibility of elliptic cross-section matrix in HGMS and providing a research clue for the development of novel high efficiency magnetic matrix for scientific researchers. The magnetic field and the flow field around the elliptic matrix are analytically calculated. The particle motion equations in the three configurations of HGMS are derived. The particle motion trajectories around the elliptic matrices are plotted. The particle capture radius and efficiency of the elliptic matrix are calculated and compared with those of the circular matrix, providing that the diameter of the circular matrix is equal to the short axis of the elliptic matrix. In the three configurations, the elliptic matrix can present higher particle efficiency than the circular matrix under some circumstances. The results indicate the promising application prospect of elliptic cross-section matrix in HGMS. The particle capture efficiency is influenced by many factors. In the development of novel high efficiency magnetic matrix, the magnetic characteristics, the flow characteristics and the arrangement of the matrix should all be taken into consideration. (C) 2016 Elsevier B.V. All rights reserved.