Support vector data description (SVDD) has been widely applied to batch process fault detection. However, it often performs poorly, especially when incipient faults occur, because it only considers the shallow data feature and omits the probabilistic information of features. In order to provide better monitoring performance on incipient faults in batch processes, an improved SVDD method, called deep probabilistic SVDD (DPSVDD), is proposed in this work by integrating the convolutional autoencoder and the probability-related monitoring indices. For mining the hidden data features effectively, a deep convolutional features extraction network is designed by a convolutional autoencoder, where the encoder outputs and the reconstruction errors are used as the monitor features. Furthermore, the probability distribution changes of these features are evaluated by the Kullback-Leibler (KL) divergence so that the probability-related monitoring indices are developed for indicating the process status. The applications to the benchmark penicillin fermentation process demonstrate that the proposed method has a better monitoring performance on the incipient faults in comparison to the traditional SVDD methods.