Better understanding of how internal short circuit causes thermal runaway will benefit the engineering for safer lithium-ion batteries. In this study, three-dimensional (3D) numerical simulations of a 20Ah lithium battery under internal shorting condition are performed. The effects of internal short circuit area, resistance, penetration depth, convective heat transfer coefficient and internal short circuit position, on the thermal runaway are investigated with the simulations in this work. This study demonstrates that the average cell temperature is only weakly affected by the internal short circuit area, penetration depth, and position. On the other hand, the internal short circuit resistance and the convective heat transfer coefficient have large impacts on the thermal runaway propagation in the lithium-ion battery. A high convective heat transfer coefficient can effectively suppress the thermal runaway propagation. However, such a high convective heat transfer coefficient is hard to achieve at the cell surface.