In the present study, an improved version of nonlinear low-Reynolds-number $k_\theta-\epsilon_\theta$ heat transfer model is proposed, in which the near-wall effect of separated and reattaching flows is fully incorporated. Emphasis is placed on the usage of $R_y$, instead of $y^+$ in the low-Reynolds-number model, together with the wall limiting behavior of the $\epsilon_\theta$ equation. As a sequence of the prior model of Park and Sung, the non-equilibrium effect ($P_\theta$/$\epsilon_\theta$) is taken into account to deal with the complex recirculation region for separated and reattaching flows away from the wall. The validation of the model is then applied to the turbulent flow behind a backward-facing step and a blunt body with separation bubble. The predicted results of the present model are compared and evaluated with the relevant experiments.