Coulomb Counting (CC) method plays an important role in the state of charge (SOC) estimation theory of lithium-ion batteries, and a lot of improvement and optimization strategies are based on it. With the increasing demand for precise management of lithium-ion battery systems, the performance of the traditional CC method is no longer suitable for more complex working conditions. First, the battery aging, extreme temperature, and high-rate discharging were considered as the main influencing factors which limit the SOC estimation accuracy of the CC method, and the performance degradation mechanism of the traditional CC method under the influence of the above factors are experimentally analyzed, especially the change of battery total dischargeable capacity after aging, and the change rules of key parameters in the CC equation are analyzed. Then the initial SOC and the total dischargeable capacity of the CC method are modified and estimated respectively to realize the accurate estimation of SOC under complex working conditions, especially the accurate SOC estimation during the whole life cycle of lithium-ion batteries. The experimental results show that the improved CC method can effectively deal with complex working conditions, and the comprehensive estimation accuracy of SOC is within 3.6%.