Against the background of magnetic detection of missile-borne control system, a new filtering method which based on FPGA was expounded due to shortcoming of traditional hardware filtering. According to the performance specification of geomagnetic data, structure and coefficients which meet the requirements of filter were designed by Matlab, and Verilog was used to complete board-level design of FP-GA. According to nonlinear characteristics of IIR filter, a phase compensation method based on phase-frequency response was put forward. Experiment has proved that filtering method based on FPGA has advantages of high speed of operation, flexible control, better filtering effect and good practicability.