In this work, a new quasi-steady state heat guarding measurement method for the thermophysical parameters of cylindrical batteries is proposed. The effectiveness of the heat guarding method is evaluated by the finite element analysis and the measurement of a standard ANSI 304 stainless steel sample. The heat loss is minimized to 2.4% maximum for cylindrical batteries under test based on numerical simulation. With the optimization of the test configuration, the experimental characterization of batteries was conducted to determine the thermal parameters accurately. The experimental results show that the axial thermal conductivity of 18650 and 21700 batteries are within 11.8–15.4 W·m−1 °C−1 and 12.6–16.7 W·m−1 °C−1, respectively, which are much lower than the material test values by the laser flash method. Axial thermal conductivity increases with temperature and SOC, and the specific heat increases linearly with temperature but varies little with SOC. This study demonstrates a fast, cost-effective and nondestructive way to obtain the axial thermal conductivity and specific heat of cylindrical batteries simultaneously and accurately. The subsequent thermal analysis on the thermal design of cylindrical batteries is also conducted based on the measured thermal parameters, which facilitate appropriate thermal management strategies for different types of cylindrical batteries.