Nail penetration into a battery pack, resulting in a state of short-circuit and thus burning, is likely to occur in electric car collisions. To demonstrate the behavior of a specific battery when subject to such incidents, a standard nail penetration test is usually performed; however, conducting such an experiment is money consuming. The purpose of this study is to propose a numerical electrochemical model that can simulate the test accurately. This simulation makes two accurate predictions. First, we are able to model short-circuited lithium-ion batteries (LIBs) via electrochemical governing equations so that the mass and charge transfer effect could be considered. Second, the temperature variation of the cell during and after nail penetration is accurately predicted with the help of simulating the temperature distribution of thermal runaway cells by thermal abuse equations. According to this nail penetration model, both the onset of battery thermal runaway and the cell temperature profile of the test are obtained, both of which are well fitted with our experimental results.