Flow boiling stands out as an efficient mode of heat transfer with significant potential for reducing carbon footprint. Based on a coupled Volume-of-Fluid and Level Set (VOSET) method, this numerical study reveals the microlayer and its evaporative heat flux distributions, as well as the effects of microlayer evaporation and depletion on bubble dynamic behavior, flow pattern, wall superheat distribution, and boiling crisis for the flow boiling in a mini-channel. These aspects are firstly comprehensively reported by the numerical method. Results indicate that the rapid evaporation of a thin microlayer positioned beneath elongated bubbles significantly contributes to heat dissipation during flow boiling in a mini-channel. The heat flux through the microlayer surpasses 300 kW/m2, accounting for approximately 42% of heat dissipation at 200 kW/m2. Furthermore, this contribution increases to over 70% as the heat flux exceeds 500 kW/m2. As a result, in comparison to scenarios without microlayers, the presence of microlayers results in an average heat transfer coefficient (HTC) that is 3.97 times larger within the range of 200–500 kW/m2. Additionally, microlayer evaporation delays the happening of flow boiling crisis. Without microlayers, the wall superheat exceeds 180 K at 500 kW/m2, whereas under microlayer influence, the maximum local wall superheat is only 37.09 K at 1000 kW/m2. With further increases in heat flux, the emergence of large dry patches resulting from microlayer depletion induces the beginning of heat transfer deterioration. Finally, the ongoing coalescence of elongated bubbles necessitates a prolonged period for rewetting dry patches at the exit of the mini-channel, triggering the flow boiling crisis at 1300 kW/m2. The study results provide crucial guidance for the development and application of the flow boiling heat transfer technology for the thermal management of data centers.