The orientation of nanomaterials with an anisotropic nature such as nanoscrolls is very important for realizing their efficient and sophisticated functions in devices, including nanostructured electrodes in artificial photosynthetic cells. In this study, we successfully synthesized a nanoscroll by intercalation of a cationic polyfluorinated surfactant into the interlayer spaces of layered niobate and successfully controlled its orientation by applying an external magnetic field in water. The exfoliated niobate nanosheets were efficiently rolled-up to form nanoscrolls, which have a fine layered structure (d₀₂₀ = 3.64 nm), by mixing with heptafluorobutanoylaminoethylhexadecyldimethylammonium bromide (C3F-S) in water, whereas the corresponding hydrocarbon analogue (C3H-S) did not form nanoscrolls. The synthetic yield for the purified and isolated nanoscrolls from the nanosheets was estimated to be 62% by weight. It was confirmed by atomic force microscopy (AFM) that most of the niobate nanosheets (98%) were converted to nanoscrolls. An external magnetic field was applied to the nanoscrolls to force them to align. After the magnetic treatment, the orientation of the nanoscrolls was investigated by small angle X-ray scattering (SAXS) and transmission electron microscopy (TEM). The non-uniform ring distribution of the SAXS patterns indicates that the nanoscrolls dispersed in water were aligned well on applying the magnetic field. The long axis of the nanoscroll was oriented in the direction of the applied field and long nanoscrolls were aligned more efficiently. When the intercalated C3F-S molecules were removed from the nanoscrolls by treating with an acid, the resultant nanoscrolls did not exhibit magnetic alignment, strongly suggesting that C3F-S plays an important role in the orientation control of the nanoscrolls by the magnetic field.