Three-dimensional simulations are performed to study the bubble breakup and boiling heat transfer in Y-shaped bifurcating microchannels with different heat fluxes and bifurcating angles. Results show that the breakup regime for continuously growing bubble changes from tunnel breakup to obstructed breakup as the heat flux increases. Interestingly, the pinch-off stage of bubble breakup becomes inconspicuous in small acute-angle bifurcating microchannel. The flow structure changes from smooth mode to twining mode as the bifurcating angle increases. The bubble transit leads to the shrink or disappearance of vortex. The heat transfer is tightly associated with bubble dynamics. The negative heat transfer enhancement is observed at low heat flux and it is eliminated at high heat flux. The heat transfer is enhanced with the increase in heat flux, while the effect of bifurcating angle is relatively complex. The present study provides new insights into the two-phase flow in bifurcating structures.