Carbon nanotube (CNT) nanofluids have promising application prospects as the working fluids in energy and power systems due to their prominent thermal properties, while the poor stability of CNT nanofluids is one of the biggest obstacles to their practical application. The addition of functional groups on CNTs is a good method to improve the dispersion of CNT nanofluids, while the influence mechanism of this strategy on the thermal transport property is not clear. In this work, the thermal conductivities of CNT, CNT-OH, and CNT-COOH nanofluids were investigated by experiments and molecular dynamics (MD) simulations to reveal the influence mechanism of functionalization on the thermal transport ability of CNT nanofluids. Both experimental measurements and MD simulations indicate the significant suppression of functionalization on the thermal transport property of CNT nanofluids. Furthermore, the influence mechanism of functional groups on the thermal conductivity of CNT nanofluids has been revealed by analyzing the effect of the thermal conductivities of CNTs, the formation of hydrogen bonds, the mean square displacement of water molecules, and the interlayer thermal resistance of CNT and water. This work is helpful to the utilization of CNT nanofluids as working fluids in energy systems.