It is necessary to select an adequate cooling technique for an electric vehicle (EV) battery module to keep the temperature within the specified range. Using a multi-scale, multi-domain electrochemical, thermal model, this paper uses a 3-dimensional CFD (Computational Fluid Dynamics) model to numerically analyze a wavy micro-channel cooling system for a high-power lithium-ion battery (LIB) module. The formulation by Newman, Tiedemann, Gu, and Kim (NTGK) model is a semi-empirical model that simulates and couples an electrochemical and thermal model to assess the cell's temperature variation through computational analysis. Semiempirical correlations are used to calculate the thermal characteristics of nanofluid (NF). The maximum temperature (T_max), temperature distribution and temperature difference (T_max − T_min) of each cell are the significant BTMS factors described in this paper. Counterflow with nanofluid controls the LIB pack's maximum temperature (T_max), temperature uniformity, and temperature difference (ΔT). The thermal performance of the battery thermal management system (BTMS) is compared while utilizing water and a water-based nanofluid (Cu 2%) as coolants. Nanofluid (Cu 2%), which has a high thermal conductivity, has a substantially more significant cooling impact than water. The suggested design with NF (Cu 2%) as coolant successfully lowers the maximum cell temperature to 305.417K. The BTMS shows a more uniform temperature distribution with counterflow in the microchannel. Although adding nanoparticles has little effect on temperature uniformity, it can drastically reduce the cell's T_max.