An integrated algorithm for analyzing the real-time, running Fourier spectra is presented. When applying to the real-time analysis, the computational efficiency and synchronization ability are highly improved by integrating the recursive procedure with the real-time implementation strategy. Given the FFT (frame) size N = 2r and moving size M = 2p, the algorithm implements the recursive procedure for updating the succeeding decomposed (into size N/M) DFTs at the (r-p)th stage, and thereafter constructs the sr-FFT (split-radix fast-Fourier-transform) butterfly modules in a real-time way. The recursive procedure highly reduces the number of complex arithmetic operations when the moving size M is small. The real-time implementation scheme enables the running spectral analysis to better synchronize with the data acquisition process. The computational complexity of the integrated algorithm is analyzed in detail, which shows the dependence of the number of complex arithmetic operations on the ratio N/M. The experimental result tested on Pentium 66 agrees with the analysis.