Downtime is a key performance index for industrial automation systems. An industrial automation system achieves maximum productivity when its downtime is reduced to the minimum. One approach to minimize downtime is to predict system faults and recover from them automatically. A cloud-based decision support system is proposed for rapid problem identifications and to assist the self-management processes. By running multiple parallel simulations of control software with real-time inputs ahead of system time, faults could be detected and corrected automatically using autonomous industrial software agents. Fault trees, as well as control algorithms, are modeled using IEC 61499 function blocks that can be directly executed on both physical controllers and cloud services. A case study of water heating process is used to demonstrate the self-healing process supported by the cloud-based decision support system.