The Hilbert spectrum images of intrinsic mode functions (IMF) of empirical mode decomposition (EMD) analysis and variational mode decomposition (VMD) analysis of faulty machine vibration signals are used in deep convolutional neural network (DCNN) for machine fault classification in which the DCNN automatically learns the features from spectral images using convolution layer. Though both EMD and VMD analysis suit well for non-stationary signal analysis, VMD has the merit of aliasing free IMFs. In this paper, the performance improvement of DCNN classification for a non-stationary vibration signal dataset using VMD is brought out. The numerical experiment uses the Hilbert spectrum images of 4 EMD-IMFs and 4 VMD-IMFs in DCNN to classify 10 different faults of the Case Western Reserve University (CWRU) bearing dataset. The confusion matrices are obtained and the plot of model accuracies in terms of epochs for the DCNN is analysed. It is shown that the spectrum images of one of the four EMD-IMFs, IMF0, give a validation accuracy of 100% and in the case of VMD the spectrum images of two of the four VMD-IMFs, IMF0, and IMF1 give a validation accuracy of 100%. This reveals that non-aliasing IMFs of VMD are better at classifying bearing faults. Further to bring out the merits of VMD analysis for non-stationary signals the numerical experiment is conducted using VMD analysis for binary fault classification of the milling dataset which is more non-stationary than the bearing dataset which is proved by plotting the statistical parameters of both datasets against time. It is found that the DCNN classification is 100% accurate for IMF3 of VMD analysis which is much better than the 81% accuracy provided by EMD analysis as per existing literature. The performance comparison highlights the merits of VMD analysis over EMD analysis and other state-of-the-art methods and ensemble learning methods.