Early recognition of abnormal rhythms in ECG signals is crucial for monitoring and diagnosing patients’ cardiac conditions, increasing the success rate of the treatment. Classifying abnormal rhythms into exact categories is very challenging due to the broad taxonomy of rhythms, noises and lack of large-scale real-world annotated data. Different from previous methods that utilize hand-crafted features or learn features from the original signal domain, we propose a novel ECG classification method by learning deep time–frequency representation and progressive decision fusion at different temporal scales in an end-to-end manner. First, the ECG wave signal is transformed into the time–frequency domain by using the Short-Time Fourier Transform. Next, several scale-specific deep convolutional neural networks are trained on ECG samples of a specific length. Finally, a progressive online decision fusion method is proposed to fuse decisions from the scale-specific models into a more accurate and stable one. Extensive experiments on both synthetic and real-world ECG datasets demonstrate the effectiveness and efficiency of the proposed method.