The disclosure herein describes a method and a system for message based communication and failure recovery for FPGA middleware framework. A combination of FPGA and middleware framework provides a high throughput, low latency messaging and can reduce development time as most of the components can be re-used. Further the message based communication architecture built on a FPGA framework performs middleware activities that would enable reliable communication using TCP/UDP between different platforms regardless of their deployment. The proposed FPGA middleware framework provides for reliable communication of UDP based on TCP as well as failure recovery with minimum latency during a failover of an active FPGA framework during its operation, by using a passive FPGA in real-time and dynamic synchronization with the active FPGA.