Severe rainstorms cause vertical mixing that modifies the internal dynamics (e.g., internal seiche, thermal structure, and velocity filed) in warm polymictic lakes. Yuan Yang Lake (YYL), a subtropical, subalpine, and seasonally stratified small lake in the north-central region of Taiwan, is normally affected by typhoons accompanied with strong wind and heavy rainfall during the summer and fall. In this study, we used the field data, statistical analysis, spectral analysis, and numerical modeling to investigate severe rainstorm-induced mixing in the lake. Statistical determination of the key meteorological and environmental conditions underlying the observed vertical mixing suggests that the vertical mixing, caused by heat loss during severe rainstorms, was likely larger than wind-induced mixing and that high inflow discharge strongly increased heat loss through advection heat. Spectral analysis revealed that internal seiches at the basin scale occurred under non-rainstorm meteorological conditions and that the internal seiches under the rainstorm were modified on the increase of the internal seiche frequencies. Based upon observed frequencies of the internal seiches, a two-dimensional model was simulated and then appropriate velocity patterns of the internal seiches were determined under non-rainstorm conditions. Moreover, the model implemented with inflow boundary condition was conducted for rainstorm events. The model results showed that the severe rainstorms promoted thermal destratification and changed vertical circulation of the basin-scale, internal seiche motion into riverine flow.