A series of cilium-like micro structures with magnetic particles embedded were fabricated for precise flow manipulation through the magnetically driven control. A hydrodynamic analysis was performed to elucidate the underlying interaction between ciliated structures and the induced flow fields. To fabricate ciliated structures, the micromachining method together with a casting process was employed. These ciliated structures were actuated in a homogeneous magnetic field generated by an in-house magnetic coil system for various beating cycles inside a microchannel. Three representative signal waveforms were created to mimic the beating nature of cilia for different flow actuating functions, such as micromixing and micropropulsion. To investigate the flow structures of induced flow fields quantitatively, a numerical modeling method using Fluid-Structure-Interaction module was performed. In addition, a micro-particle image velocimetry (μPIV) experiment was conducted to characterize the nonreciprocal movement of ciliated structures for the quantification of hydrodynamic efficiency. By means of the presented analysis paradigms, a new flow manipulation strategy will be suggested to transport/agitate flows efficiently in microfluidics.