The invention provides an Ethernet application layer protocol control system based on hardware acceleration. An FPGA performs protocol analysis on application layer network protocol packets, matches the analysis result by utilizing a plurality of parallel protocol identification algorithms, executes a corresponding control operation according to the matching result, discards or forwards the application layer network protocol packets which do not need to be subjected to deep processing, and transmitting the application layer network protocol packets which need to be subjected to deep processingto a CPU for processing; and the FPGA receives and forwards a processing result returned by the CPU to realize protocol control of the application layer. According to the system, a software and hardware combination mode is adopted, the communication connection between the FPGA and the CPU is added, a process of analyzing and processing application layer network protocol packets in a CPU in the prior art is transferred to an FPGA to be realized, the application layer network protocol packets are processed in parallel through the FPGA, and the application layer network protocol packets needingto be processed by the CPU are captured and intercepted and are transmitted back to the CPU for processing, so that the burden of the CPU is greatly reduced, the Ethernet application layer protocol control efficiency is improved, and CPU acceleration is realized.