Rod matrix is effectively applied in pulsating high gradient magnetic separation (PHGMS), due to its reliable operation, simple combination and resistance to mechanical entrainment. The matrix is made of huge numbers of rod elements and as a whole its configuration presents a decisive role in the operation of PHGMS, due to the fact that it has an inherent determination on the distribution of magnetic field in the matrix and on the collision efficiency of particles with the matrix, thus producing a dominant control on the dynamics of magnetic particles in the matrix and on the separation performance of PHGMS. An experimental approach entitled Slice Matrix Analysis (SMA) method is developed and attempted to optimize the configuration of rod matrix, with a cyclic pilot-scale PHGMS separator in concentrating fine hematite. It was found that the configuration has a significant effect on the separation performance of PHGMS, and the SMA method provides an effective way for the optimization of rod matrix.