The optimized microchannel heat sinks could enhance flow boiling for effectively tackling the electronics cooling. The flow boiling experiment for three microchannel heat sinks integrated with different layouts of entrenched pin fins is conducted at flow rate of 273.6–456 kg/(m2.s) and inlet subcooling of 35∼50 K. The overall/local heat transfer features, pressure drop and boiling mechanism are studied. The hybrid pattern presents earliest initial boiling and lower superheat than the microchannel heat sink with uniform pin fins arrangement at moderate and large flow rates. The trend of overall and local HTC (heat transfer coefficient) is similar, which occurs peak at onset nucleation boiling, and then decreasing with increasing heat flux. At the largest flow rate, the hybrid pattern exhibits 2.7–3.5 times peak HTC promotion than other patterns. As for lowest flow rate, the hybrid pattern does not manifest remarkably superior performance due to downstream vapor cores clogging effect. The hybrid pattern shows largest pressure drop, and the smaller inlet subcooling manifests inferior heat transfer and resistance performance. The comprehensive performance factor (CPF) is proposed, and the pattern with uniform small-sized pin fins shows optimal CPF especially for low flow rate, which is considerable compared with the reference heat sink structures until high heat flux. This study may provide some insight into the design of microchannel for flow boiling heat dissipation.