Pin fins have been widely applied in microchannels to enhance the heat transfer performance, however, they inevitably lead to a large increase in the pressure drop and the pump power consumption, which hinders their practical applications in microchannel heat sinks. In this work, we report that lowering the pin fin to channel height ratio can significantly reduce the pressure drop while largely maintaining the heat transfer enhancement for flow boiling in finned microchannels. A novel two-step deep reactive ion etching (DRIE) approach is developed to fabricate finned microchannel heat sinks with the controllable pin fin to channel height ratio. Our results show that at low to moderate heat flux, all the microchannel heat sinks with pin fins show nearly overlapping boiling curves, as pin fins elevate flow boiling heat transfer through enhanced bubble nucleation in this heat flux range, which is not affected by the height of pin fins. However, higher pin fins lead to a larger heat transfer coefficient (HTC) in the high heat flux range and a higher critical heat flux (CHF), which can be attributed to the enlarged surface area and the increased flow velocity. Importantly, compared to the microchannel heat sink with full-height pin fins, the pressure drop can be significantly reduced by 43.9 % through lowering the pin fin height ratio to 50 %, while the CHF is only slightly decreased by 10.1 %. The performance evaluation criterion (PEC) analysis shows that the calculated PEC is larger than 1 for lower pin fins at most heat flux conditions, which confirms that lowering the pin fin to channel height ratio is beneficial for flow boiling in finned microchannels. Moreover, flow reversal is effectively suppressed due to the increased flow resistance and the confinement of bubble growth by pin fins. This work sheds the light on the design of finned microchannel heat sinks with high flow boiling heat transfer performance and reduced pressure drop.