The intricate role of temperature in the structure-property relationship of manganese oxide nanoparticles (Mn3O4 NPs) remains an open question. In this study, we successfully synthesized Mn3O4 NPs using the hydrothermal method with two differing temperatures, namely, 90 and 150 °C. Interestingly, a smaller average particle size is found when Mn3O4 NPs are synthesized at 150 °C compared to 90 °C, corresponding to 46.54 and 63.37 nm, respectively. This was confirmed by the time variation of temperature setting of 150 °C where the size evolution was insignificant, indicating a competing effect of nucleation and growth particles. Under varying NaOH concentrations (2-6 M) at 150 °C, a reduction in the particle size is found at the highest NaOH concentration (6 M). The particle grows slightly, indicating that the growth state is dominant compared to the nucleation state at low concentrations of NaOH. This finding implies that the high nucleation rate originates from the excessive monomer supply in the high-temperature reaction. In terms of crystallinity order, the structural arrangement of Mn3O4 NPs (150 °C) is largely decreased; this is likely due to a facile redox shift to the higher oxidation state of manganese. In addition, the higher ratio of adsorbed oxygen and lattice oxygen in Mn3O4 NPs at 150 °C is indirectly due to the higher oxygen vacancy occupancies, which supported the crystallinity decrease. Our findings provide a new perspective on manganese oxide formation in hydrothermal systems.