Infrared signature analysis that considers both the target and background is fundamentally important to the development of target detection systems as well as in the design of ships for thermal stealth. This paper presents the analysis results of long-term infrared signature variations in terms of the apparent spectral-contrast radiant intensity measured using Fourier transform infrared (FTIR)-based hyperspectral images. A novel apparent spectral-contrast radiant intensity (AS-CRI) measure is proposed to evaluate the spectral infrared signature accurately at the sensor point of view. The spectral information by AS-CRI can provide the optimal band for either target detection or thermal stealth purposes, considering the background and atmospheric transmittance. In addition, the effects of seasonal and weather variations were analyzed from the long-term hyperspectral image database constructed during 2018.01–2018.08 (three times a day). A TELOPS HYPER-CAM MWE camera was adopted to acquire 374 bands in 1.5–5.5 μm. The automatic weather system (AWS) can provide 24 h weather recordings for the signature evaluation. The experimental results validate the utility of the novel AS-CRI method to find spectral bands for a range of infrared signature applications including small infrared target detection.