According to the accuracy and speed requirements of battery State of Charge measurement for online monitoring, this paper presents a battery system identification based on Fuzzy Identification Algorithm. And through the analysis of battery State of Charge and internal resistance, voltage-side data, the fuzzy rule model of battery State of Charge is built. The measuring mean square error of the model is 0.0052. Measurement results show that method for the State of Charge of the battery measuring based on Fuzzy Identification Algorithm can battery-line monitoring to meet the requirements, and easily implemented in hardware. The article also use the DSP Builder to design the battery State of Charge measurement module, where the resistance was measured using the signal feature extraction method based on Eigendecomposition Spectrum Estimation,and State of Charge measurement is to achieve the uses of the fuzzy rule model derived from Fuzzy Identification Algorithm.