In this paper we optimise the performance of microchannel heat sink with upper flow arrangement of flow at entrance and exit. The performance of micro channel heat sink is directly affected by the pumping power and the thermal resistance. Here we flow from the upper section and optimise to be very low pumping power and thermal resistance. The aspect ratio and the hydraulic diameter of the microchannel are same for flow arrangement. Fluid flow and heat transfer are investigated on the basis of the simulation of the micro channel with number of channel in rectangular shapes. The aim of this work is to get an impression of the physical behaviour in small elements that enable the development of new liquid cooling systems with higher cooling ability and higher effectiveness.