Aiming at the problems of detection, which exists in the analysis of inter-harmonics applying all-phase time-shift phase difference correction method, an inter-harmonic detection method based on APFFT and fast TLS-ESPRIT is proposed in this paper. In this algorithm, first of all, the frequency of inter-harmonics is accurately identified by the fast TLS-ESPRIT algorithm. Then, the signal is analyzed through APFFT algorithm. According to the phase invariance, the phase value of the peak spectral line is directly used as the initial phase estimation. Finally, the frequency deviation of peak line is calculated and the amplitude estimate of the signal is obtained according to the all-phase amplitude correction formula. Simulation shows that the proposed algorithm is effective under a low SNR environment, and it can detect inter-harmonics of a given signal much more accurately.