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Three simple capping molecules (urea, 3‐aminopropanol, and polyethylene glycol) with different functional groups (−NH2 for urea, −NH2 and −OH for 3‐aminopropanol, and −O− for polyethylene glycol) have been designed to prepare magnetite (Fe3O4) particles with various shapes. The crystal structure, morphologies, and magnetic properties of the products have been characterized by X‐ray diffraction, electron microscopy, and vibrating sample magnetometer. The results indicate that the capping functional groups play a major role in determining the size, shape, and thus magnetic properties of the magnetite nanocrystals. The morphology evolution of the magnetite under the hydrothermal condition is discussed in detail, particularly for the interaction between the various capping groups and surface structure and chemistry of the nanocrystals.