The thermal evolution of neutron stars (NSs) is investigated by coupling with the evolution of $\textit{r}$-mode instability that is described by a second order model.The heating effect due to shear viscous damping of the $\textit{r}$-modes enables us to understand the high temperature of two young pulsars (i.e., PSR B0531+21 and RX J0822-4300) in the framework of the simple $npe$ NS model, without superfluidity or exotic particles.Moreover, the light curves predicted by the model within an acceptable parameter regime may probably cover all of the young and middle-aged pulsars in the $\lg T_s^{∞}-\lg t$ panel, and an artificially strong $p$ superfluidity invoked in some early works is not needed here. Additionally, by considering the radiative viscous damping of the $\textit{r}$-modes, a surprising extra cooling effect is found, which can even exceed the heating effect sometimes although plays an ignorable role in the thermal history. Comment: 12 pages, 3 figures