Output performance of a thermoelectric-based automotive waste heat recovery system with a nanofluid coolant is analyzed in this study. Comparison between Cu-Ethylene glycol (Cu-EG) nanofluid coolant and ethylene glycol with water (EG-W) coolant under equal mass flow rate indicates that Cu-EG nanofluid as a coolant can effectively improve power output and thermoelectric conversion efficiency for the system. Power output enhancement for a 3% concentration of nanofluid is 2.5-8 W (12.65-13.95%) compared to EG-Water when inlet temperature of exhaust varies within 500-710 K. The increase of nanofluid concentration within a realizable range (6%) has positive effect on output performance of the system. Study on the relationship between total area of thermoelectric modules (TEMs) and output performance of the system indicates that optimal total area of TEMs exists for maximizing output performance of the system. Cu-EG nanofluid as coolant can decrease optimal total area of TEMs compared with EG-W, which will bring significant advantages for the optimization and arrangement of TEMs whether the system space is sufficient or not. Moreover, power output enhancement under Cu-EG nanofluid coolant is larger than that of EG-W coolant due to the increase of hot side heat transfer coefficient of TEMs.