Concerning the low classification accuracy of Motor Imagery ElectroEncephaloGram(MI-EEG), a new Convolutional Neural Network(CNN) model based on deep framework was introduced. Firstly, the time-frequency information under two resolutions was obtained by using Short-Time Fourier Transform(STFT) and Continuous Wavelet Transform(CWT). Then, it was combined with the channel position information and used as the inputs of the CNN in the form of three-dimensional tensor. Secondly, two network models based on different convolution strategies, namely MixedCNN and StepByStepCNN, were designed to perform feature extraction and classification recognition of the two types of inputs. Finally, in order to solve the problem of overfitting due to insufficient training samples, the mixup data augmentation strategy was introduced. Experimental results on BCI Competition Ⅱ dataset Ⅲ showed that the model performed highest accuracy by training the CWT samples reconstructed by mixup data augmentation on MixedCNN(93.57%), which was 19.1%, 20.2%, 11.7% and 2.3% higher than those of the other four analysis methods including Common Spatial Pattern(CSP) + Support Vector Machine(SVM), Adaptive Autoregressive Model(AAR) + Linear Discriminant Analysis(LDA), Discrete Wavelet Transform(DWT) + Long Short-Term Memory(LSTM), STFT + Stacked AutoEncoder(SAE). The proposed method can provide a reference for MI-EEG classification tasks.