The rapid development of modern communication technology makes the identification of emitter signals more complicated. Based on Ward's clustering and probabilistic neural networks method with correlation analysis, an ensemble identification algorithm for mixed emitter signals is proposed in this paper. The algorithm mainly consists of two parts, one is the classification of signals and the other is the identification of signals. First, self-adaptive filtering and Fourier transform are used to obtain the frequency spectrum of the signals. Then, the Ward clustering method and some clustering validity indexes are used to determine the range of the optimal number of clusters. In order to narrow this scope and find the optimal number of classifications, a sufficient number of samples are selected in the vicinity of each class center to train probabilistic neural networks, which correspond to different number of classifications. Then, the classifier of the optimal probabilistic neural network is obtained by calculating the maximum value of classification validity index. Finally, the identification accuracy of the classifier is improved effectively by using the method of Bivariable correlation analysis. Simulation results also illustrate that the proposed algorithms can accurately identify the pulse emitter signals.