Ultrafine amorphous Fe-B alloy nanoparticles are self-assembled within anodic aluminum oxide templates by combining a preparation process of Fe-B nanoparticles with a template method. Scanning electron microscopy, inductively coupled plasma-atomic emission spectrometry, X-ray diffraction spectrometry, Mossbauer spectrometry, and vibrating sample magnetometry are employed to study the morphology, chemical composition, structure, and magnetic properties of the nanoparticle assemblies, respectively. The results show that the alloy particles are amorphous with a boron content of 24 at. % and can be in shape of sphere and rod by controlling the duration of preparation. There is a narrow distribution of the sizes of spherical nanoparticles with an average diameter below 35 nm in relatively short preparation time, while rods are found in longer time. The measurements of magnetic properties indicate that the nanoparticles are mostly in superparamagnetic state and the self-assembly of the nanoparticles has a weak magnetic anisotropy with an easy direction perpendicular to the template plane.