The bundled structure of micron-sized pectin gel filaments was formed by quick shear-induced gelation of the filamentous domains of pectin-polyethylene glycol (PEG) assemblies. Highly concentrated pectin with PEG in a separated pectin-rich phase under aqueous two-phase separation in the pectin/PEG/NaCl system enabled the formation of the pectin-PEG assembly, which was elongated in the flow direction, resulting in the generation of filamentous domains using a microfluidic device. The pectin gel filaments were formed by crosslinking with Ca2+ in the presence of shear-responsive PEG assemblies formed in the PEG-rich phase, because the filamentous PEG assemblies prevented fusion of the pectin filaments to form the seamless cylindrical gel. The shear-dependent elongation applied to the pectin-PEG assembly under the aqueous two-phase separation condition enabled the formation of the biomimetic bundled filamentous structure using bio-safe PEG as a sacrificial polymer, without the requirement of a multi-hole nozzle. Potential applications for gel filaments possessing a bundled structure are matrices in the biomedical field, such as a biodegradable scaffold for cell engineering.