A three-dimensional ultrasound tomography method and system based on spiral scanning are provided. The method includes the following. (1) Collecting raw data: an emission array element is switched while a probe maintains a uniform linear motion, so that changes in trajectory with time of a position of an equivalent emission array element in a three-dimensional space show a spiral or a partial spiral, and echo data is received. (2) Pre-processing data. (3) Calculating coordinates of each equivalent emission array element. (4) Calculating coordinates of an imaging focus point. (5) Performing synthetic aperture focusing on each imaging focus point. (6) Post-processing data. The disclosure improves the principle of the imaging method, the design of the overall process, etc. Volume data containing information of continuous tissue layers is obtained through spiral scanning. Applying the synthetic aperture focusing technique in the three-dimensional space improves the resolution between layers and shorten the scan time.