Coolant is one of the important factors affecting the overall performance of the intercooler for the intercooled (IC) cycle marine gas turbine. Conventional coolants, such as water and ethylene glycol, have lower thermal conductivity which can hinder the development of highly effective compact intercooler. Nanofluids that consist of nanoparticles and base fluids have superior properties like extensively higher thermal conductivity and heat transfer performance compared to those of base fluids. This paper focuses on the application of two different water-based nanofluids containing aluminum oxide (Al2O3) and copper (Cu) nanoparticles in IC cycle marine gas turbine intercooler. The effectiveness-number of transfer unit method is used to evaluate the flow and heat transfer performance of intercooler, and the thermophysical properties of nanofluids are obtained from literature. Then, the effects of some important parameters, such as nanoparticle volume concentration, coolant Reynolds number, coolant inlet temperature, and gas side operating parameters on the flow and heat transfer performance of intercooler, are discussed in detail. The results demonstrate that nanofluids have excellent heat transfer performance and need lower pumping power in comparison with base fluids under different gas turbine operating conditions. Under the same heat transfer, Cu–water nanofluids can reduce more pumping power than Al2O3–water nanofluids. It is also concluded that the overall performance of intercooler can be enhanced when increasing the nanoparticle volume concentration and coolant Reynolds number and decreasing the coolant inlet temperature.