The emergence of microfluidic techniques provides new opportunities for chemical synthesis and biomedical applications. Herein, we first develop a microfluidics-based flow and sustainable strategy to synthesize hierarchical silica-magnetic microflower with unique multilayered structure for the efficient capture of circulating tumor cells through our engineered microfluidic screening chip. The production of microflower materials can be realized within 94 milliseconds and a yield of nearly 5 grams per hour can be achieved. The enhanced bioaccessibility of such a multilayered microflower towards cancer cells (MCF-7 and MDA-MB-231) is demonstrated, and the cancer cell capture efficiency of this hierarchical immunomagnetic system in clinical blood samples is significantly increased compared with a standard CellSearch™ assay. These findings bring new insights for engineering functional micro-/nanomaterials in liquid biopsy.