Thermal hazards of the surrounding rock of subway tunnels are becoming apparent, in which the heat transfer in the surrounding rock plays a crucial role. Due to the shallow buried depth, the subway tunnel encounters a more complicated heat exchange under the duplicate effects of periodic temperature fluctuation of ground atmosphere and periodic temperature variation of tunnel wind, but this issue has not been fully addressed. In this work, a transient heat transfer model of tunnel surrounding rock based on dual periodic temperature boundaries was established. A solver was developed to estimate the temperature rise and heat transfer of surrounding rock. The correctness of this model was then verified by comparing with previous empirical values and semi-empirical equations. The results show that the temperatures of the surrounding rock at different depths still fluctuate following the simple harmonic waves, and there are some regions that are heavily affected by the duplicate effects, such as the overlying strata of the tunnel. The surrounding rock generally exhibits heat storage in annual cycle, but the total heat storage decreases year by year until it tends to stabilize. Furthermore, the shallower the tunnel is buried, the greater the influence of ground temperature and the higher the temperature rise in the tunnel surrounding rock. This research provides an alternative approach to determine the heat storage of tunnel surrounding rock and evaluates the process of thermal disaster manifestation of subway.