To satisfy the require of the MRI main control board, this paper puts forwards a new design which uses FPGA development board as main control board and uses Nios II as a coprocessor. We transplant the μC/OSII operating system and protocol stack lwIP to achieve the network communication with computers. Then we use the hardware language Verilog to write pulse sequence generation module to achieve the analysis and execution of the command. Eventually it produces user's pulse sequence. Final test results show that the communication rate of the main control board and pulse sequence which is obtained by oscilloscope can satisfy the requirements of the MRI system. Compared with the past of the whole software design, this design make the MRI system higher precision and more stable.