The main objective of the present paper is to investigate the effect of using connecting holes on the hydrothermal performance and irreversibility behavior of laminar forced convection flow of a nanofluid (NF) inside a microchannel heat sink (MCHS). The biologically synthesized silver/water NF is employed as coolant. The influences of the volume concentration of NF (φ), the Reynolds number (Re) and the number of connecting holes on the performance features of MCHS and NF are considered numerically. It was observed that the CPU temperature is reduced and became more uniform due to boosting of Re and φ, and the consequence augmentation of the convective heat transfer. However, the pumping power and frictional irreversibility get raised as Re and φ are increased. The figure of merit is above unity for all Re and φ which indicate that the utilization of connecting holes is a suitable option to improve the MCHS performance from the first-law point of view. The heat transfer irreversibility, however, increased by using the connecting holes. Also, the merit of NF over the pure water is observed for Re of 500 and 2000 and φ of 0.1% and 1%.