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To apply Fiber Bragg Grating (FBG) sensors in the hole structural health monitoring of aircraft, this study investigates a temperature compensation algorithm based on Fourier curve-fitting, combined with an analysis of FBG layout. The results identify that the wavelengths have a linear relationship with stress and temperature and the linear correlation coefficients are all greater than 0.9. In the experiment, the temperature range was 17 °C-100 °C (step is 10 °C) and the tensile force changed from 0 N to 10 KN (step is 1 KN). With the Fourier curve-fitting of the wavelength variation, the temperature compensation can be actualized, and the average error of temperature is 0.17 °C. By integrating the algorithm in the self-developed FBG interrogation system, the real-time monitoring of stress is achieved with the average error of stress is 3.9 με.