We report the generation of harmonic noise-like mode-locked pulses in a thulium-doped fiber laser. In this laser, mode-locking can be realized through the nonlinear polarization rotation (NPR) technique. The ring cavity configuration uses 5 m of a Tm-doped dual-cladding fiber, as a gain medium, pumped by a 793 nm diode laser. The cavity uses a couple of polarization controllers (PCs) and polarization-dependent isolator to form a nonlinear polarization-rotating saturable absorber. By carefully adjusting of the PCs, the laser generates noise-like mode-locked pulses at the 2.04 μm band. With the increase of the pump power, the laser generates harmonics of the mode-locking fundamental repetition frequency of 6.88 MHz, from which we can obtain the second harmonic in a controlled mode. The obtained results may be useful for enhancing the understanding of the mechanism and characteristics of noise-like pulse at the 2 μm band.