In this paper, the characteristics of the flickering pixel phenomenon in the infrared scanning image are analyzed. The detection and compensation method of the flickering pixel based on the time series multi-frame maximum projection is designed. Considering that the flickering pixels still retain a part of the information acquisition ability, the one-dimensional median filter is used to suppress the background for the position where flickering pixels exist. Traditional methods of target detection are carried out for the image after flickering pixels compensated. Experiment results show that after background suppression, the target average signal to clutter ratio in the flickering pixel location can reach 96% of the normal position, and the target information is well preserved. The traditional method of target detection is no longer interfered by flickering noise.