Efficient cell manipulation is essential for numerous applications in bioanalysis and medical diagnosis. However, the lack of stability and strength in the secondary flow, coupled with the narrow range of practical throughput, severely restricts the diverse applications. Herein, we present an innovative inertial microfluidic device that employs a spiral channel for high-throughput cell manipulation. Our investigation demonstrates that the regulation of Dean-like secondary flow in the microchannel can be achieved through geometric confinement. Introducing ordered microstructures into the ultralong spiral channel (>90 cm) stabilizes and accelerates the secondary flow among different loops. Consequently, effective manipulation of blood cells within a wide cell throughput range (1.73 × 108 to 1.16 × 109 cells/min) and cancer cells across a broad throughput range (0.5 × 106 to 5 × 107 cells/min) can be achieved. In comparison to previously reported technologies, our engineering approach of stabilizing and accelerating secondary flow offers specific performance for cell manipulation under a wide range of high-throughput manner. This engineered spiral channel would be promising in biomedical analysis, especially when cells need to be focused efficiently on large-volume liquid samples.