In this paper, the intelligent estimation algorithm is developed for residual quantity estimate of lithium secondary cell and we suggest the control algorithm to get battery SOC through thermal modeling of electric cell. Lithium secondary cell gives cycle life, charge characteristic, discharge characteristic, temperature characteristic, self-discharge characteristic and the capacity recovery rate etc. Therefore, we make an accurate estimate of the capacity of battery according to thermal modeling to know the capacity of electric cell that is decreased by various special quality of lithium secondary cell. And we show effectiveness through comparison of value as result that use simulation and fuzzy logic.