<p>The microstructural features and hydrophilic properties of surfaces are crucial in enhancing boiling heat transfer efficiency, offering a viable strategy for the thermal management of high-power electronic systems. However, conventional macroscopic experimental techniques and numerical simulations make it difficult to reveal the phase change process of a liquid at the microscopic scale. Consequently, this study applies molecular dynamics simulation methods to explore the phase transition behaviors of liquid water on hydrophilic nano-grooved surfaces at the nanoscale. By comprehensively analyzing the nucleation dynamics, bubble volume evolution, energy variation of water molecules within the thin liquid layer beneath the bubble, variations in heat flux during bubble growth, and the molecular motion characteristics and energy transfer mechanisms of nucleate boiling on shallow grooved structures are elucidated. The findings indicate that during bubble growth, a gradually thinning liquid layer forms beneath the bubbles. Furthermore, according to the bubble volume curve, the critical bubble radius is determined to be 1.59–1.95 nm. As the bubble volume increases, the average potential energy of the thin liquid layer exhibits a downward trend. Particularly, during bubble nucleation, the heat flux of the substrate exceeds 8×10⁻³ eV·nm⁻²·ps⁻¹. When the bubble appears, the heat flux rises; however, it decreases when a vapor film forms. The investigation of the thin liquid layer beneath the bubble not only deepens the understanding of energy transfer mechanisms during the nucleate boiling zone but also provides theoretical guidance for designing efficient heat sink components.</p>