To solve the problem of small infrared target detection under complex backgrounds, an effective algorithm based on saliency analysis in frequency domain is proposed. The infrared target is usually more significant than backgrounds in spectral domain. Thus, we can obtain the saliency map of the infrared image through some operations in frequency domain. In this way, target signal is enhanced and background clutter is suppressed. Then, an adaptive threshold is adopted to segment the saliency map and extract the region of interest. At last, the saliency of windows in the region of interest is measured to predict the exact position of the small targets. Theoretical analysis was made to the effectiveness of the algorithm. And to validate our algorithm, we conducted experiments on some typical infrared images that contain small targets. Experimental evaluation results show that our method can implement infrared small target detection under low signal-to-noise ratio fairly well, and the method is simple, effective, and can satisfy the real-time requirement while guaranteeing the detection accuracy.