Previously we introduced a novel hydrodynamic method using a multi-orifice microchannel for size-based particle separation, which is called a multi-orifice flow fractionation (MOFF). The MOFF has several advantages such as continuous, non-intrusive, and minimal power consumption. However, it has a limitation that the recovery yield is relatively low. Although the recovery may be increased by adjusting parameters such as the Reynolds number and central collecting region, poor purity inevitably followed. We newly designed and fabricated a microfluidic channel for multi-stage multi-orifice flow fractionation (MS-MOFF), which is made by combining three multi-orifice segments, and consists of 3 inlets, 3 filters, 3 multi-orifice segments and 5 outlets. The structure and dimensions of the MS-MOFF were determined by the hydrodynamic principles to have constant Reynolds numbers at each multi-orifice segment. Polystyrene microspheres of two different sizes (7 μm and 15 μm) were tested. With this device, we made an attempt to improve recovery and minimize loss of purity by collecting and re-separating non-selected particles of the first separation. The final recovery successfully increased from 73.2% to 88.7% while the final purity slightly decreased from 91.4% to 89.1% (for 15 μm). These values were never achievable with the single-stage MOFF (SS-MOFF) having only one multi-orifice segment in our previous work. The MS-MOFF channel will be useful for clinical applications, such as separation of circulating tumor cells (CTC) or rare cells from human blood samples.