Thermal effects could dramatically destroy the performances of the orthogonal-polarized He-Ne laser featured with an integrated Y-shaped cavity. To explore detailed impacts on the output frequency difference stability, one thermal model was established via the ANSYS software. Material disposals and heat source loading were presented, including the calculations of heat flux density and transfer coefficients. Thermal features were shown and discussed both in steady-state and transient-state. Later practical experiments were employed with a thermal infrared imager. The differences between simulations and experimental results were barely smaller than 1%, which had validated the accuracy and reliability of the simulations. After the laser setting to work, heat gradually transmitted from gain area to non-gain area. When the temperature distribution of the laser was in steady state, the cavity surface regions had maximum thermal gradient. The points maximum temperature were always near the cathode, while those with minimum temperature were close to the underlying surfaces of the sub-cavities. The temperature difference was about 0.05 ℃ between the surfaces of the sub-cavities, and the resulted frequency drift was about 0.067 MHz. It reveals that the time-dependent temperature divergences between two sub-cavity is still the main restricting factor in the stability of the laser output frequency difference, which can provide some important guidance for improving the stability of laser frequency difference and optimizing the design of laser geometry construction.