In order to improve the recognition accuracy and efficiency of power quality disturbances (PQD) in microgrids, a novel PQD feature selection and recognition method based on optimal multi-resolution fast S-transform (OMFST) and classification and regression tree (CART) algorithm is proposed. Firstly, OMFST is carried out according to the frequency domain characteristic of disturbance signal, and 67 features are extracted by time-frequency analysis to construct the original feature set. Subsequently, the optimal feature subset is determined by Gini importance and sorted according to an embedded feature selection method based on the Gini index. Finally, one standard error rule subtree evaluation methods were applied for cost complexity pruning. After pruning, the optimal decision tree (ODT) is obtained for PQD classification. The experiments show that the new method can effectively improve the classification efficiency and accuracy with feature selection step. Simultaneously, the ODT can be constructed automatically according to the ability of feature classification. In different noise environments, the classification accuracy of the new method is higher than the method based on probabilistic neural network, extreme learning machine, and support vector machine.