How to improve the classification accuracy is a key issue in four-class motor imagery-based brain-computer interface (MI-BCI) systems. In this paper, a method based on phase synchronization analysis and common spatial pattern (CSP) algorithm is proposed. The proposed method embodies the idea of the inverted binary tree, which transforms the multi-class problem into several binary problems. First, the phase locking value (PLV) is calculated as a feature of phase synchronization, then the calculated correlation coefficients of the phase synchronization features are used to construct two pairs of class. Subsequently, we use CSP to extract the features of each class pair and use the linear discriminant analysis (LDA) to classify the test samples and obtain coarse classification results. Finally, the two classes obtained from the coarse classification form a new class pair. We use CSP and LDA to classify the test samples and get the fine classification results. The performance of method is evaluated on BCI Competition IV dataset IIa. The average kappa coefficient of our method is ranked third among the experimental results of the first five contestants. In addition, the classification performance of several subjects is significantly improved. These results show this method is effective for multi-class motor imagery classification.