The present work reports a clear and improved hydrothermal methodology for the synthesis of MoSe2 nanoflowers (MNFs) at 210 °C. To observe the effect of temperature on the fascinating properties, the process temperature was modified by ±10 °C. The as-prepared MNFs were found to consist of 2D nanosheets, which assembled into a 3D flower-like hierarchical morphology via van der Waals forces. The elemental composition and mapping of the MNFs reveal that the constituents are uniformly distributed throughout the material. Crystallographic and structural analyses confirmed that the as-synthesized MNFs were of a highly crystalline nature with a two-layer hexagonal (2H) phase of MoSe2 (2H-MoSe2). Additionally, the microstructure and lattice-scale features of the MNFs studied using HRTEM disclosed ultrathin nanosheets of thickness ∼3 nm, which were a few atomic layers thick. A plausible formation and growth mechanism of the as-prepared MNFs is also proposed. For the purpose of developing supercapacitors, the electrochemical energy storage characteristics of the synthesized MNFs were examined. Maximum specific capacitance of 284.8 F g-1 at 5 mV s-1 scan rate was demonstrated by the three-electrode setup, and the capacitance retention was about 88%, even after 10 000 cycles. As an electrode material for supercapacitors, MNFs have great potential due to their high specific capacitance and exceptional cycling stability.