Recently, a variety of intelligent structural damage identification algorithms have been developed and have obtained considerable attention worldwide due to the advantages of reliable analysis and high efficiency. However, the performances of existing intelligent damage identification methods are heavily dependent on the extracted signatures from raw signals. This will lead to the intelligent damage identification method becoming the optimal solution for actual application. Furthermore, the feature extraction and neural network training are time-consuming tasks, which affect the real-time performance in identification results directly. To address these problems, this paper proposes a new intelligent data fusion system for damage detection, combining the probabilistic neural network (PNN), data fusion technology with correlation fractal dimension (CFD). The intelligent system consists of three modules (models): the eigen-level fusion model, the decision-level fusion model and a PNN classifier model. The highlight points of this system are these three intelligent models specialized in certain situations. The eigen-level model is specialized in the case of measured data with enormous samples and uncertainties, and for the case of confidence level of each sensor is determined ahead, the decision-level model is the best choice. The single PNN model is considered only when the data collected is somehow limited, or few sensors have been installed. Numerical simulations of a two-span concrete-filled steel tubular arch bridge in service and a seven-storey steel frame in laboratory were used to validate the hybrid system by identifying both single- and multi-damage patterns. The results show that the hybrid data-fusion system has excellent performance of damage identification, and also has superior capability of anti-noise and robustness.