The invention discloses a microgrid energy storage SOC estimation method and a system based on a least square support vector machine. Firstly, a microgrid experiment platform comprising an energy storage system is used, and through measurement, voltage, current, temperature and an SOC data sequence of the energy storage system during a charging and discharging process are obtained; according to the measurement data, training set and test set samples for the least square support vector machine are obtained; a cross validation method is then used for selecting the optimal training parameters for the training set of the least square support vector machine, and a training model is further obtained; and the testing set is then used for testing the training model, the result is evaluated, and finally, the training model can be used for SOC estimation determination on the corresponding type of energy storage system in the microgrid. Defects in the traditional SOC calculation method can be overcome, reference is provided for charging and discharging control on the energy storage system, deep charging and discharging of a battery can be prevented, and the service life of the battery and the operation safety of the microgrid can be improved.