A novel design is presented to defend against electromagnetic interference (EMI) in a high speed data acquisition system. Problems that affect signal integrity (SI) in high speed image acquisition systems, such as reflection, crosstalk and groundbounce, are deeply analyzed in a manner consistent with transmission line theory. The results can theoretically inform EMI design of important networks, including system power, ground, clocks, high speed wires and decoupling capacitors. Experiments simulating print circuit board(PCB) reflection and EMI on high speed signal wires between DM642 and SDRAM are conducted. The power and ground should be placed separately in different layers. The clock lines passing through holes should be as few as possible. The signal lines should be as close to the same length as possible. The results show that amplitude of the signal overshoot is less than 0.7 V and the EMI amplitude is within the federal communications commission(FCC) standard.