Thermal stratification is a key physical process controlling carbon flux from lakes to the atmosphere. Vertical profiles in shallow subtropical lakes can vary greatly because typhoons frequently induce vertical mixing across the entire lake due to strong winds and rapid river flushing from inputs. Since carbon fluxes are driven by Dissolved Inorganic Carbon (DIC), it is necessary to clarify the effect of stratification on DIC dynamics in shallow subtropical lakes to estimate carbon fluxes. Therefore, we aim to clarify the influence of stratification on DIC in Yuan-Yong Lake that is a typical shallow subtropical lake. We measured the vertical profile of water temperature every month from July 2004 to December 2017. We applied a three-dimensional hydrological model to estimate net ecosystem production by combining with endmember analysis, suggesting the possibility that large amount of DIC is stored in the lower layer from spring to summer due to the suppression of vertical mixing by stratification. In autumn, DIC was diluted across the layers because of strong vertical mixing due to typhoons. Vertical profiles of DIC in winter were confirmed to be uniform due to overturning.