Within the context of industry 4.0, the personalized customization requires the manufacture more agile and flexible, which means the reconfigurable manufacturing system is crucial for enterprise to remain competitive. However, most of the existing systems have to suspend when reconfiguring, as the online reconfiguration may lead system to disorder and uncertainty. To minimize the leading time of reconfiguration while ensuring system stability, this paper proposes a solution based on an industrial pipeline structure by utilizing IEC 61499 Function Blocks combined with Multi-agent systems and ontology. And a simulation is conducted to verify the effectiveness of this solution.