In the chromatic measuring system, a kind of optical fiber probe was added to collect the light to decrease the interference to the reflected light from the object. But the probe brings the distortion to the system in the chromatic measurement. This paper put forward a method based on the Fourier Transform to compensate the non-linear attenuation of the fixed length optical fiber. In the scope of visible light, with a series of experiments, an adjustable function for the optical fiber probe is obtained. Using this adjustable function, the error of fiber-optic transmission can be lowed less than 1%. At the same time, the chromatic coordinate was tested with the fiber probe and without the probe. The error of the chromatic coordinate is below 0.01, and it meets the international standard criteria in chromatic measurement. It is proved that this method is suitable for compensating of the fixed length optical fiber's chromatic compensation.