A two dimensional electrochemical thermal model is developed on the cross-plane of a laminate stack plate pouch lithium ion battery to study the thermal performance of large format batteries. The effect of thermal contact resistance is taken into consideration, and is found to greatly increase the maximum temperature and temperature gradient of the battery. The resulting large temperature gradient would induce in-cell non-uniformity of charging-discharging current and state of health. Simply increasing the cooling intensity is inadequate to reduce the maximum temperature and narrow down the temperature difference due to the poor cross-plane thermal conductivity. Pulse charging protocol does not help to mitigate the temperature difference on the bias of same total charging time, because of larger time-averaged heat generation rate than constant current charging. Suggestions on battery geometry optimizations for both prismatic/pouch battery and cylindrical battery are proposed to reduce the maximum temperature and mitigate the temperature gradient within the lithium ion battery.