We synthesized manganese oxide (MnO and Mn3O4) nanocrystals with various sizes and shapes by the thermal reaction of a MnII–oleate complex through a “heat‐up process”. When a MnII–oleate complex was thermally decomposed in non‐coordinating hydrocarbon solvents, uniformly sized MnO nanocrystals with cubic and octahedral shapes were produced. We were able to synthesize anisotropic, multibranched MnO nanocrystals by the oriented attachment of MnO truncated‐nanocube building blocks. When the MnII–oleate complex was heated in 1‐hexadecene in the presence of strongly coordinating carboxylic acid surfactants, spherical nanocrystals were generated, and their diameter was controlled in the range 3–13 nm by varying the chain length of the carboxylic acid. When oleyl alcohol was added to the Mn–oleate complex in phenyl ether, tetrahedral MnO nanocrystals were synthesized. The as‐synthesized MnO nanocrystals were oxidized in air to Mn3O4 or MnO/Mn3O4 core–shell structures, which exhibited exchange coupling with shifted magnetic hysteresis loops. The effect of the size and shape of the phospholipid‐capped manganese oxide nanocrystals on their applicability as T1 contrast agents in magnetic resonance imaging (MRI) were examined. As the size of the nanocrystals decreased, their relaxivities increased, thereby generating brighter MR images. In particular, spherical 3 nm‐sized Mn3O4 nanocrystals had a high specific relaxivity (r1) of 2.38 mM–1 s–1, clearly demonstrating their potential for use as an efficient T1 MRI contrast agent.