Temperature variation is a key factor affecting the stability of fiber optic frequency transfer systems. In a long-distance optical fiber frequency transfer system, a dispersion compensation fiber (DCF) placed in the machine room and a non-buried single-mode fiber (SMF) are collectively referred to as a bare optical fiber. Due to the impact of the external environment, the temperature of the bare optical fiber varies drastically, which seriously deteriorates the long-term stability (10,000 s stability) of the frequency transfer system. To investigate the relationship between the temperature variation of the bare optical fiber and the frequency transfer stability, we use VPItransmissionMaker optical simulation software to simulate and study the fiber frequency transfer system of the bare optical fiber under the impact of different temperatures. The simulation found that the system stability is 1.4  ×  10^−  16  /  10⁴  s in a 3000 km link when the temperature variation of DCF is 5°C, whereas the impact on the system stability is on the order of 10^−  16  /  10⁴  s when the length of the non-buried SMF is more than 300 km and the temperature variation is more than 10°C. To verify the correctness of the simulation, the stability of the actual 80 km fiber optic frequency transfer system was compared with that of the simulation, and the stability of the simulation was found to be 4.2  ×  ^{10  −  17}  /  ¹⁰⁴s, whereas the stability of the experimentally measured system was 7.9  ×  10^−  17  /  10⁴  s, and the simulation results were basically consistent with the experimental results.