An improved algorithm named "twice-FFT" for multi-point intrusion location in distributed Sagnac sensing system is proposed and demonstrated. To find the null-frequencies more accurately and efficiently, a second FFT is applied to the frequency spectrum of the phase signal caused by intrusion. After Gaussian fitting and searching the peak response frequency in the twice-FFT curve, the intrusion position could be calculated out stably. Meanwhile, the twice-FFT algorithm could solve the problem of multi-point intrusion location. Based on the experiment with twice-FFT algorithm, the location error less than 100m for single intrusion is achieved at any position along the total length of 41km, and the locating ability for two or three intrusions occurring simultaneously is also demonstrated.