In this paper, a Hammerstein state of charge (SOC) estimation model for lithium-ion batteries with two inputs and single output is constructed to map the relation between battery SOC and its discharge current/voltage, and a key-term separation based least square (KT-LS) algorithm is studied to identify the model parameters so as to identify the battery SOC. The thought is, by adopting the key-term separation principle, to decompose the key-term from the linear element and to substitute the expression of the nonlinear element only into the decomposed key-term, thus to express the model output as a linear auto-regression form about parameters. Then the least square algorithm is performed to optimize parameters in the reformed auto-regression form of the Hammerstein SOC system. The advantages of the explored the KT-LS algorithm contains the least parameters required, thus the calculation burden of the KT-LS algorithm is small compared with the over-parameterized model based algorithm. In the simulation experiment part, the performance of the KT-LS algorithm under different conditions are analyzed under UDDS and LA92 conditions.; the performance comparison between the KT-LS algorithm and the key-term separation based stochastic gradient (KT-SG) algorithm is carried out; the performance of the KT-LS algorithm based Hammerstein model method is compared with that of the back propagation (BP) neural network, the Long Short Term Memory (LSTM) neural network and the Extended Kalman filter (EKF) method. The simulation results show that the KT-LS algorithm based Hammerstein SOC model can effectively estimate the SOC of lithium-ion batteries.