The polarization control of non-polarization maintaining fiber amplifier is an effective way to obtain high power linear polarization fiber laser output. In this paper, we introduce the principle of optical fiber amplifier polarization control based on stochastic parallel gradient descent (SPGD) algorithm, and also numerically analyze the effects of the parameters, such as algorithm performance evaluation function, influence of disturbance voltage distribution types, gain step and the disturbance amplitude on polarization control. Then we use field programmable gate logic array (FPGA) to perform SPGD algorithm, and control the polarization state of the output light. Finnaly, the obtained polarization extinction ratio of the output laser is greater than 11 dB.