Schizophrenia (ScZ) is a devastating mental disorder of the human brain that causes a serious impact of emotional inclinations, quality of personal and social life and healthcare systems. In recent years, deep learning methods with connectivity analysis only very recently focused into fMRI data. To explore this kind of research into electroencephalogram (EEG) signal, this paper investigates the identification of ScZ EEG signals using dynamic functional connectivity analysis and deep learning methods. A time-frequency domain functional connectivity analysis through cross mutual information algorithm is proposed to extract the features in alpha band (8-12 Hz) of each subject. A 3D convolutional neural network technique was applied to classify the ScZ subjects and health control (HC) subjects. The LMSU public ScZ EEG dataset is employed to evaluate the proposed method, and a 97.74 ± 1.15% accuracy, 96.91 ± 2.76% sensitivity and 98.53 ± 1.97% specificity results were achieved in this study. In addition, we also found not only the default mode network region but also the connectivity between temporal lobe and posterior temporal lobe in both right and left side have significant difference between the ScZ and HC subjects.