It is very difficult to multiplex fiber Fabry-Perot sensor because of its fundamental limitation. When serially multiplexed, it is especially complicated due to mutual affection between sensors. To address this problem, the simplest case of two fiber Fabry-Perot (F-P) sensors multiplexed in series was discussed. According to the principle of double beam interference, the output of serially multiplexed sensors was derived, and its characteristics was discussed in detail. Fourier transform was adopted to transform the output from wavelength domain into spatial frequency domain. The dissatisfaction of conditions for using Fourier transform signal processing of fiber Fabry-Perot senor was discussed, and distortion of Fourier transform was analyzed. With the simulation of Fourier transform, the eigenvalues of two fiber Fabry-Perot sensor were demultiplexed in spatial frequency domain. In addition, experiment of serial multiplexing two fiber Fabry-Perot sensors was carried out. The experimental results showed that, Fourier transformation in demultiplexing serially multiplexed fiber Fabry-Perot sensors was valid, and mutual affection between two fiber Fabry-Perot sensors was less than 5%.