To improve temperature distribution is uneven in Y-shaped microchannel (Y) heat sink, connected Y-shaped microchannel (CY) is proposed and heat dissipation performance is compared. Results revealed that CY model has a lower peak temperature and makes temperature distribution more uniform due to two symmetrical vortexes are formed at both sides of branch structure, while there are still high temperature zones in the second stage channels under high heat flux. Therefore, the micro pin fins are embedded in CY heat sink (FCY) to examine heat transfer performance. Results illustrated that there is more pressure loss in FCY heat sinks, while temperature uniformity of FCY model is better than CY heat sink, which strengthens heat dissipation of the second stage channels. Heat transfer coefficients of FCY-1, FCY-2 and FCY-3 heat sinks are 1.12, 1.28 and 1.11 times than CY model, respectively. The composite performance factor, both FOM2/1 and FOM2/3 are greater than 1. The FCY-2 model demonstrates a good thermal and hydraulic performance can achieve the best cooling capacity.