A novel cross-flow based particle sorter is proposed and demonstrated in this study. The filtration structures consist of two groups of micropillars that are fabricated with photoresist material SU-8 using the femtosecond laser induced two-photon polymerization (TPP) technique. Particles can be separated according to the slit sizes of the micropillars. The distributions of flow velocity and particle trajectories in filters of different lengths are simulated with the COMSOL software. The particle sorting efficiencies are calculated and compared. The microfluidic sorter chip is tested with a fluid consisting of mixed microbeads with diameters of 10 μm and 5 μm. The performance of the sorter developed in this study demonstrates its effectiveness and efficiency in sorting particles in a fluid. Furthermore, the femtosecond laser induced TPP microfabrication technique enables the fabrication of customized microstructures with a high degree of integration and low fabrication cost, promising for various biological, chemical, and environmental applications.