The invention discloses a system of a CPU and a logic module to do the data transmission in an embedded system and a method. The CPU is connected with the logic module by a PCI bus. The logic module comprises a PCI device standard interface unit, a data receiving interface unit, a data sending interface unit, a control unit and a protocol processing unit. When the data needs sending, the CPU notifies the logic module to obtain the data from the address designated by the CPU in a caching descriptor and to send the data, and sends a sending interruption to the CPU; when the logic module receives the data, the protocol processing unit does the protocol process on the received data and transmits the data to the caching position pointed by the current caching descriptor as well as sends a receiving interruption to the CPU. In the data transmission process, the invention does not need the participation of the CPU, thereby effectively reducing the seizure rate of the CPU.