Heterostructure rough spindle‐knot microfibers (HRSFs) are fabricated via a flexible parallel‐nozzle microfluidic method. In this method, the bioinspired HRSF with a roughness gradient between spindle‐knots and joints, can be manufactured in large‐scale, and with which the size of the spindle‐knots and joints can be precisely adjusted by regulating flow rates. The HRSFs, fabricated with chitosan and calcium alginate, have strong mechanical properties and corrosion resistance in acid environment (pH = 5) and alkaline environment (pH = 9), respectively. More attractively, under controlled treatment conditions, the morphology of the spindle‐knots on the HRSFs can be effectively managed by changing the composite content of calcium chloride in the fluid. During the water collection process, tiny droplets of moisture can be captured on the surface of the HRSFs, subsequently, the droplets can coalesce and be transported from joint to spindle‐knot sections. It is demonstrated that the surface morphology of spindle‐knots directly influences the water collection efficiency, where a higher roughness gradient generates higher water collection efficiency. This parallel‐nozzle microfluidic technology provides a low‐cost and flexible method to manufacture high biocompatibility bioinspired rough spindle‐knot microfibers, which has many potential applications in large‐scale water collection, sustained drug release, and directional water collection.