This study numerically investigated the symmetric breakup of bubble within a heated microfluidic Y-junction. The established three-dimensional model was verified with the results in the literature. Two crucial variables, Reynolds number (Re) and heat flux (q), were considered. Numerical results demonstrated that the bubble breakup was significantly affected by phase change under the heated environment. The “breakup with tunnel” and “breakup with obstruction” modes respectively occurred at the low and high q. The breakup rate in pinch-off stage was much larger than that in squeezing stage. As Re increased, the bubble broke more rapidly, and the critical neck thickness tended to decrease. The bubble annihilated the vortices existing in the divergence region and made the fluid flow more uniform. The heat transfer was enhanced more drastically as Re was decreased or q was increased, where the maximum Nusselt number under two-phase case was 6.53 times larger than single-phase case. The present study not only helps understanding of the physical mechanisms of bubble behaviors and heat transfer within microfluidic Y-junction, but also informs design of microfluidic devices.