The conjugate heat transfer and the thermal stresses produced within a pin-fin microchannel heat sink are investigated numerically. The pin-fin microchannel heat sink is subjected to a constant heat flux from the bottom surface and cooled by water flow through the channel across the pin fins. Rectangular cross-section microchannel incorporating one raw of square pin fins are considered. The water flowing through the microchannel at Reynolds number varies from 200 to 800. The heat sink dissipates constant heat flux in the range of 75-175 kW/m2. The selected materials used for the solid substrate are Copper, Aluminium, Titanium, and Structural steel. The results are presented as contour plots for the temperature, thermal stress, and deformation distribution. It is found that the heat dissipation and the Nusselt number are increased with increasing Reynolds number, increasing the thermal conductivity of the material but remain constant throughout various heat fluxes. Thermal stresses are increased with decreasing Reynolds number, increasing heat flux, and increasing Youngs’ Modulus of the substrate material. The total deformation is increased with decreasing Reynolds number, increasing heat flux, and increasing the thermal expansion coefficient of the substrate material.