We propose a model of lithium secondary batteries for analyzing both charging/ discharging characteristics and the increase of cell temperature in the case of the internal short circuit. We give an explanation to the experimental results of the nail penetration tests and discuss the structure-dependent properties of the batteries from the viewpoint of balance between energy density and safety. In particular, it is suggested that the thermal runaway in the nail penetration tests is determined by the total amount of Joule heat produced by the large current due to the internal short circuit until the discharge of the whole electrode is completed.