Two-phase closed thermosyphon as a gravity-assisted heat pipe is an efficient heat transfer device in which heat transmits by evaporation and condensation of a working fluid. Nanofluids are suspensions of nano-sized solid particles in a base fluid which can be used as heat transfer media in the thermosyphon. In the present study, thermal performance of functionalized multi-walled carbon nanotubes/water nanofluids was investigated in a novel type of thermosyphon which was made of an evaporator with square frustum shape, and a condenser composed of two connected tubes. To prepare nanofluids, multi-walled carbon nanotubes were first functionalized using two oxidant agents (potassium persulfate and sodium persulfate) to improve the cooling performance of nanofluids. The prepared nanofluids were characterized by Fourier transform infrared spectroscopy, inductively coupled plasma optical emission spectroscopy, zeta potential, and thermal conductivity analyzer. The results of characterization showed that the nanofluid with sodium functional group had higher stability as well as higher thermal conductivity. Thermal efficiency and thermal resistance were calculated to evaluate the thermal performance of thermosyphon. Using nanofluid with sodium functional group in the thermosyphon showed better performance in terms of higher thermal efficiency and lower thermal resistance. Experimental results also showed that the thermosyphon could perform at higher input powers (up to 90 W) using the nanofluid compared to water (up to 70 W). Furthermore, the results of the temperature distribution of thermosyphon during the test confirmed that two connected tubes in the condenser section could provide pathways for both condensate liquid and vapor. In other words, this behavior indicated that this type of thermosyphon can be considered between a tubular thermosyphon and a loop thermosyphon.