The invention relates to an ellipsoid expansion-based three-dimensional seismic data stacking velocity calculation method. The method comprises the following steps: common-normal emergent point bins are divided with a work region, and the position of each bin is determined; the position where the center of the bin is located serves as an analysis point, a common-normal emergent point collection at the analysis point is extracted; ellipsoid expansion is carried out on the basis of a three-dimensional relationship equation of the seismic data space and the stacking data space and a velocity spectrum is calculated; the root mean square velocity is picked in the velocity spectrum; the root mean square velocity of each analysis point is obtained through repeating the above steps on all bin analysis points; and through carrying out interpolation and extrapolation on the root mean square velocity of each analysis point, a stacking velocity field at the study region is built. The obtained stacking velocity field is accurate and reliable, a high-precision initial velocity field can be provided for the migration velocity analysis method, main reflection events of the obtained zero-offset stacking profile is complete in levels, distinct in wave group features and high in signal-to-noise ratio.