Abstract: In order to broadcast precise ephemeris data with high speed, code shift keying (CSK) modulation is likely to be adopted in next generation satellite navigation system. The correlation values of various code phase offsets are needed during demodulation, so the frequency domain demodulation algorithm based on fast Fourier transform (FFT) is usually used. According to the characteristic that only partial output are needed in CSK frequency domain demodulation, an efficient demodulation algorithm for CSK signal based on partial output FFT is proposed in this paper. The algorithm optimizes the butterfly-shaped structure of traditional FFT, and reduces the computational complexity of demodulation by defining computing nodes to eliminate invalid computations irrelevant to the output results. Taking the CSK(4,1023) modulated signal with a code rate of 1.023 Mcps as an example, the algorithm proposed in this paper can reduce about 45.6% of the calculation, which is of great significance to the design of the next generation satellite navigation receiver.