The invention discloses a data transmission system based on FPGA and a transmission method thereof. The PS module is arranged and a PL module comprising an SRIO module, an LVDS module and a PS module-PL module, a DMA module and a FIFO memory is also arranged, the SRIO module and the LVDS module are used to transmit and receive data, at that same time, the data is stored in the FIFO memory, the DMAmodule receives a PS module for accessing data in the FIFO memory, various control and data calculation are carried out within that PS module, while in the PL module, it is mainly used for data transmission and control, reduces the amount of logic control in the PL module, make the whole design clear and simple, DMA module is used to realize the data transmission between PS module and PL module,reducing consumption on the bus. With a burst of transmission like DMA, the number of initiation operations of the PS module is reduced, and the DMA transmission mode does not require the participation of the PS module in the data moving process, the PS module is free from the data move work, the program in the PS module is optimized, and more time is provided for data processing at the same time.