In order to eliminate the influence of polarization-induced fading and polarization-induced phase shift on the positioning performance in a dual Mach-Zehnder interferometry disturbance sensing system, a polarization control method based on field programmable gate array (FPGA) with simple structure and high efficiency is proposed. The method adopts polarization controller feedback technology and uses feedback values of two optical signals as control functions. In combination with the improved harmony search (IHS) algorithm, the FPGA hardware parallel structure and pipeline technology are used to rapidly implement the algorithm iteration and control the polarization controller to adjust the polarization state. The experimental results show that the method can adjust the polarization state of the system in a short time, the polarization control time is about 0.7808 s, and the positioning error of the system is improved up to within ±20 m, which effectively eliminate the polarization effect on the positioning performance. Besides, the use of FPGA instead of the computer as the control core of the system improves the data processing speed, reduces the polarization control time, and improves the integration of system, thereby facilitating the miniaturization of the polarization control instruments.