Robotic-assisted rehabilitation system based on Brain-Computer Interface (BCI) is an applicable solution for stroke survivors with a poorly functioning hemiparetic arm. The key technique for rehabilitation system is the feature extraction of Motor Imagery Electroencephalography (MI-EEG), which is a nonlinear time-varying and nonstationary signal with remarkable time-frequency characteristic. Though a few people have made efforts to explore the nonlinear nature from the perspective of manifold learning, they hardly take into full account both time-frequency feature and nonlinear nature. In this paper, a novel feature extraction method is proposed based on the Locally Linear Embedding (LLE) algorithm and DWT. The multiscale multiresolution analysis is implemented for MI-EEG by DWT. LLE is applied to the approximation components to extract the nonlinear features, and the statistics of the detail components are calculated to obtain the time-frequency features. Then, the two features are combined serially. A backpropagation neural network is optimized by genetic algorithm and employed as a classifier to evaluate the effectiveness of the proposed method. The experiment results of 10-fold cross validation on a public BCI Competition dataset show that the nonlinear features visually display obvious clustering distribution and the fused features improve the classification accuracy and stability. This paper successfully achieves application of manifold learning in BCI.