In this paper, crystalline iron-nickel alloy nanostructures were successfully prepared from two cationic pyridinium derivatives as soft templates in solution. The crystal structure and micrograph of FeNi alloy nanostructures were characterized by X-ray diffraction, scanning electron microscopy and transmission electron microscopy, and the content was confirmed by energy-dispersive spectrometry. The results indicated that the as-prepared nanostructures showed slightly different diameter ranges with the change of cationic pyridinium derivatives on the surface. The experimental data indicated that the adsorption of cationic pyridinium compounds on the surface of particles reduces the surface charge, leading to an isotropic distribution of the residual surface charges. The magnetic behaviours of as-prepared FeNi alloy nanostructures exhibited disparate behaviours, which could be attributed to their grain sizes and distinctive structures. The present work may give some insight into the synthesis and character of new alloy nanomaterials with special nanostructures using new soft templates.