Endwall fillet and bulb structures are proposed in this research to improve the temperature uniformity of pin-fined microchannels. The periodical laminar flow and heat transfer performances are investigated under different Reynolds numbers and radius of fillet and bulb. The results show that at a low Reynolds number, both the fillet and the bulb structures strengthen the span-wise and the normal secondary flow in the channel, eliminate the high temperature area in the pin-fin, improve the heat transfer performance of the rear of the cylinder, and enhance the thermal uniformity of the pin-fin surface and the outside wall. Compared to traditional pin-fined microchannels, the flow resistance coefficient f of the pin-fined microchannels with fillet, as well as a bulb with a 2 µm or 5 µm radius, does not increase significantly, while, f of the pin-fined microchannels with a 10 µm or 15 µm bulb increases notably. Moreover, Nu has a maximum increase of 16.93% for those with fillet and 20.65% for those with bulb, and the synthetic thermal performance coefficient TP increases by 16.22% at most for those with fillet and 15.67% at most for those with bulb. At last, as the Reynolds number increases, heat transfer improvement of the fillet and bulb decreases.