Numerical results of the thermal and hydraulic characteristics of pulsating laminar flow in a three-dimensional helical microchannel heat sink (HMCHS) filled with a porous medium using Al2O3–water based nanofluid are presented in this paper. The two-phase mixture model with modified effective thermal conductivity and viscosity equations were used to solve the laminar flow governing equations. The detailed results for thermal and flow fields are reported for the effects of amplitude (1–3) and frequency (5–20rad/s). The presence of porous media led to better thermal enhancement and significant improvement in heat transfer performance was observed for sinusoidal velocity inlet conditions as compared to steady flow conditions. In addition, the proposed model showed better accuracy in predicting nanofluid flow.