For multi-source high speed parallel data real-time transmission problems in data association network, a multi-source data optical transmission system based on sampling clock recovery is presented in this paper, and its operating principle and design idea are introduced in detail. The system combines the high speed transceiver in Field Programmable Gate Array (FPGA) with the special digital phase-locked loop chip, and gives the specific scheme of sampling clock recovery and data flow control. Compared with the existing high speed parallel data transmission system, the one presented in this paper has software-defined access capability and supports more flexible dynamic range for the different sampling clock. What is more, through the design of simplified and reasonable frame structure, and the constraint relation between the data bit width and the sampling clock is deduced, the system can improve the effective transmission bandwidth obviously. The test results show that this system can work stably and reliably with an excellent real-time transmission effect, and have the high precision of clock recovery. Meanwhile the system extends the application field of serializer and deserializer technology, and it provides a high reference value for other transmission systems.