The electrocardiogram (ECG) is widely used for cardiovascular disease diagnosis and daily health monitoring. Before ECG analysis, ECG quality screening is an essential but time-consuming and experience-dependent work for technicians. An automatic ECG quality assessment method can reduce unnecessary time loss to help cardiologists perform diagnosis. This study aims to develop an automatic quality assessment system to search qualified ECGs for interpretation. The proposed system consists of data augmentation and quality assessment parts. For data augmentation, we train a conditional generative adversarial networks model to get an ECG segment generator, and thus to increase the number of training data. Then, we pre-train a deep quality assessment model based on a training dataset composed of real and generated ECG. Finally, we fine-tune the proposed model using real ECG and validate it on two different datasets composed of real ECG. The proposed system has a generalized performance on the two validation datasets. The model’s accuracy is 97.1% and 96.4%, respectively for the two datasets. The proposed method outperforms a shallow neural network model, and also a deep neural network models without being pre-trained by generated ECG. The proposed system demonstrates improved performance in the ECG quality assessment, and it has the potential to be an initial ECG quality screening tool in clinical practice.