The sizes of most prokaryotic cells are several microns. It is very difficult to separate cells with similar sizes. A sorter with a contraction–expansion microchannel and applied magnetic field is designed to sort microparticles with diameters of 3, 4 and 5 microns. To evaluate the sorting efficiency of the designed sorter, numerical simulations for calculating the distributions of microparticles with similar sizes were carried out for various magnetic fields, inlet velocities, sheath flow ratios and structural parameters. The numerical results indicate that micro-particles with diameters of 3, 4 and 5 microns can be sorted efficiently in such a sorter within appropriate parameters. Furthermore, it is shown that a bigger particle size and more powerful magnetic field can result in a greater lateral migration of microparticles. The sorting efficiency of microparticles promotes a lower inlet velocity and greater sheath flow ratios. A smaller contraction–expansion ratio can induce a greater space between particle-bands. Finally, the micro particle image velocity (micro-PIV) experiments were conducted to obtain the bandwidths and spaces between particle-bands. The comparisons between the numerical and experimental results show a good agreement and make the validity of the numerical results certain.