To reveal the key optimization considerations for the application of elliptic cross-section matrices in axial high gradient magnetic separation (HGMS), the performance of circular and elliptic matrices was investigated experimentally and theoretically, providing that the short axis of elliptic matrix was equal to the diameter of circular matrix. Three schemes were adopted to investigate the performance matrices with ratio of long axis to short axis λ of 1 (circular matrix), 1.6 and 2. Under the same matrix unit number, hematite recovery of elliptic matrices could be 5~20% higher than that of circular matrices. For the case that the separation space was fully filled under the same matrix unit spacing, elliptic matrices showed higher and lower hematite recovery in low and relatively high magnetic field. The particle capture cross section area of elliptic matrix could be 1.4~1.8 times larger than that of circular matrix. Analyses with particle capture models showed that higher hematite recovery was ascribed to the larger particle capture cross section of the elliptic matrices and overlapping of the capture cross section was responsible for the lower hematite recovery of elliptic matrices in relatively high magnetic field. For substitution of circular matrices with elliptic matrices in axial HGMS, overlapping of capture cross section of target particles should be taken into consideration.