Using conventional methods to synthesize magnetic nanoparticles (NPs) with uniform size is a challenging task. Moreover, the degradation of magnetic NPs is an obstacle to practical applications. The fabrication of silica-shielded magnetite NPs on carbon nitride nanotubes (CNNTs) provides a possible route to overcome these problems. While the nitrogen atoms of CNNTs provide selective nucleation sites for NPs of a particular size, the silica layer protects the NPs from oxidation. The morphology and crystal structure of NP–CNNT hybrid material is investigated by transmission electron microscopy (TEM) and X-ray diffraction. In addition, the atomic nature of the N atoms in the NP–CNNT system is studied by near-edge X-ray absorption fine structure spectroscopy (nitrogen K-edge) and calculations of the partial density of states based on first principles. The structure of the silica-shielded NP–CNNT system is analyzed by TEM and energy dispersive X-ray spectroscopy mapping, and their magnetism is measured by vibrating sample and superconducting quantum interference device magnetometers. The silica shielding helps maintain the superparamagnetism of the NPs; without the silica layer, the magnetic properties of NP–CNNT materials significantly degrade over time.