Ion beam sputtering machine uses computer to real time monitor the change of film thickness in the preparation process of soft X ray multilayer element fabrication. It solves the problems of uneven film thickness and too thick film thickness and so on, which exist in the original preparation process. The high-precision quartz crystal converts film thickness measurement into frequency measurement. The equal precision frequency meter based on FPGA measures the frequency. It can reduce the signal delay and interference signal of discrete components, accordingly improving the accuracy of measurement. Then it sents the count value to the host computer through the single chip microcomputer serial port. It calculates and displays the value by the GUI of LabVIEW. The experimental results show that, the relative measurement error can be decreased to 1/10, i.e., the measurement accuracy can be improved by more than ten times.