Microchannel heat exchangers (MCHE) can be designed with different channel geometry such as circular, triangular, rectangular, square, trapezoidal and hexagonal. In this article, the influence of channel geometry on thermal, hydraulic and overall performance of counter flow MCHE operated on CuO-water nanofluid flow has been highlighted. Herein, Nusselt and Poiseuille number for different channel shapes and thermo-physical properties of CuO-water nanofluid (viz., thermal conductivity, viscosity…) have been designed either empirically or adopted from literature. Results of pumping power with trapezoidal geometry MCHE is found to be highly sensitive with nanofluid flow. Rectangular shape counter flow MCHE gives highest thermal effectiveness, while iso-triangular geometry gives best overall performance by converting the pressure energy into thermal energy.