A 3D (Three-Dimensional) electrochemical-thermal model has been developed to study internal short circuits in a 1 Ah Li-ion cell, which was inspired by the new findings from the controlled internal short tests. Noteworthy difference of the temperature profiles at the short spot were observed between a Anode–Aluminum (current collector) shorting test and a Anode–Cathode shorting test, with the former showing a temperature spike upon incurring short circuit while the later not. Modeling study reveals that the rapid temperature increase observed in the Anode–Aluminum short was the result of high rate discharge while the following sudden temperature drop was due to the lithium transport limitations in the solid and electrolyte phases. By contrast, in the Anode–Cathode short, such limitations were not observed as the discharge rate was much lower. The results of the present study may help design a safer Li-ion cell through the understanding of a specific internal short circuit.