J wave is getting more and more important in the clinical diagnosis as a new index of the electrocardiogram (ECG) of ventricular bipolar, but its signal often mixed in normal ST segment, using the traditional electrocardiograph, and diagnosed by experience cannot meet the practical requirements. Therefore, a new method of multilayer nonnegative matrix factorization (NMF) in this paper is put forward, taking the hump shape J wave, for example, which can extract the original J wave signal from the ST segment and analyze the accuracy of extraction, showing the characteristics of hump shape J wave from the aspects of frequency domain, power spectrum, and spectral type, providing the basis for clinical diagnosis and increasing the reliability of the diagnosis of J wave.