The heat flow behavior of lithium-ion batteries during normal operation is an important consideration for safety. Yet, there are few studies on this subject. In current work, the heat flow of Li(Ni1/3Co1/3Mn1/3)O2 (NCM) and LiFePO4 (LFP) batteries during a discharge and charge cycle at different ambient temperatures and discharge rates has been tested for the first time using a high precision isothermal microcalorimeter (TAM IV). The agreement of the measured heat flow over several repeated cycles is excellent, with a spike in heat flow occurring at the end of discharge. Low temperatures have a greater effect on the heat flow of the battery than high temperatures. NCM batteries have greater thermal stability than LFP batteries during heating and cooling, as well as when the discharge rate increases. Meanwhile, the heat flow spike of NCM batteries has a good exponential dependence on temperature and discharge rate. At a certain temperature, a model of the heat flow eigenvalue function, which is only dependent on the discharge rate, is developed. There is a strong correlation between the heat flow behavior and the electrical behavior of LFP and NCM batteries. The research provides a practical basis for the application, monitoring, and optimization of lithium-ion batteries.