A selective preparation and the formation mechanism of hexagonal and cubic CoO nanoparticles from the reaction of [Co(acac)2] (acac=acetylacetonate) and amine have been investigated. CoO nanoparticles with a hexagonal pyramidal shape were yielded under decomposition conditions with amine. Importantly, the addition of water altered the final phase to cubic and comprehensively changed the reaction mechanism. The average sizes of the hexagonal and cubic CoO nanoparticles could be controlled either by changing the amine concentration or by using different reaction temperatures. Detailed formation mechanisms are proposed on the basis of gas chromatography–mass spectrometry data and color changes of the reaction mixture. The hexagonal CoO phase is obtained through two distinct pathways: solvolysis with CC bond cleavage and direct condensation by amine. On the other hand, the cubic CoO nanoparticles were synthesized by strong nucleophilic attack of hydroxide ions from water and subsequent CC bond breaking. The resulting caboxylate ligand can stabilize a cobalt hydroxide intermediate, leading to the generation of a thermodynamically stable CoO phase.