In our previous paper (J L Xu et al 2005 J. Micromech. Microeng. 15 362–76), it is identified that the transient flow patterns for microscale boiling heat transfer are repeated on the timescale of milliseconds. A full cycle could be subdivided into three substages: liquid refilling stage, bubble nucleation, growth and coalescence stage and transient annular flow stage. Five heat transfer mechanisms could be deduced from the transient flow patterns. This paper extends the above work and mainly focuses on the boiling heat transfer behavior, which was performed for 102 runs with the following data ranges: inlet pressures of 1–2 bar, inlet liquid temperatures of 24–45 °C, pressure drops of 10–100 kPa, mass fluxes of 64–600 kg m⁻² s⁻¹, heat fluxes of 150–480 kW m⁻², exit vapor qualities of 0.07–1.15 and the boiling numbers of 0.69 × 10⁻³–5.046 × 10⁻³. The silicon wafer test section consists of ten triangular microchannels with the hydraulic diameter of 155.4 µm. Acetone is selected as the working fluid. The heat transfer coefficients were analyzed with the effects of the heat fluxes, the mass fluxes and the vapor mass qualities. We provide a link between the transient flow patterns and the heat transfer process. The boiling numbers can be used to characterize the microscale boiling heat transfer, which can display three distinct regions by dividing the boiling numbers into three subranges. The transient flow pattern based heat transfer mechanisms are very consistent with the heat transfer coefficient measurements with the effects of the heat fluxes, mass fluxes and vapor mass qualities. The transition boundaries among the three heat transfer regions are given.