As the process of informatization progresses in an equipment manufacturing enterprise, its information system becomes a dissipative structure due to the nonlinear interaction of many factors. The objectives of this study were to help enterprises adopt intelligent manufacturing, realize sustainable development strategies, and understand the operation rules of information systems. For this purpose, this study analyzed an anomaly index time series of an information system in the process of integration. First, the embedding dimension, time delay, average period, and maximum Lyapunov exponent of the time series were calculated. The anomaly index with chaotic characteristics was denoised by combining phase space reconstruction with singular value decomposition (SVD). Finally, a radial basis function (RBF) neural network and local nonlinear method were used to predict the anomaly index of 79 test data points. The case simulation results verify that the anomaly index is affected by changes in basic data, system development, and online migration. One instance of local noise reduction can reveal hidden problems in the actual operations of enterprises, and multiple iterations can extract the actual information of the signals, avoid failures at isolated points, and show a clear attractor structure. Both the RBF neural network and local nonlinear approach are effective prediction methods with low relative errors, but the performance of the latter is superior.