This research examines how the positioning of obstacle heights affects the smooth flow of a water and silver nanoparticle mixture inside a rectangular microchannel, which has 0 to 4 % nanoparticles mixed in Simulations are done numerically using two-phase and finite volume approaches for Reynolds numbers between 1 and 150. Heat fluxes that change over time are applied to the walls made of silicon in the microchannels to study this research. The findings show that different obstacle heights change the flow and heat transfer along the channel. Notably, the setup with obstacles decreasing in height on the hot wall (case 1) achieves the highest average Nusselt number. On the other hand, the obstacles increasing in height (case 3) yield the largest pressure drop and friction, leading to the highest performance evaluation criterion (PEC). Lastly, the uniform obstacle height positioning leads to the least pressure drop.