In the present study, we numerically demonstrate an approach for separation of micro and sub-micro diamagnetic particles in dual ferrofluid streams based on negative magnetophoresis. The dual streams are constructed by an intermediate sheath flow, after which the negative magnetophoretic force induced by an array of permanent magnets dominates the separation of diamagnetic particles. A simple and efficient numerical model is developed to calculate the motions of particles under the action of magnetic field and flow field. Effects of the average flow velocity, the ratio of sheath fluid flow to sample fluid flow, the number of the magnet pair as well as the position of magnet pair are investigated. The optimal parametric condition for complete separation is obtained through the parametric analysis, and the separation principle is further elucidated by the force analysis. The separation of smaller micro and sub-micro diamagnetic particles is finally demonstrated. This study provides an insight into the negative magnetophoretic phenomenon and guides the fabrication of feasible, low-cost diagnostic devices for sub-micro particle separation.