The invention belongs to the crossing field of physical oceanography and computer graphics and image processing, and particularly relates to a mesoscale eddy tracing method based on a hybrid algorithm. The hybrid algorithm mainly comprises nearest neighbor search, deformation control based similarity match and delay logic. The method comprises the following steps: step one, for the nearest neighbor search, eddies in a search range are delineated according to global mesoscale eddy data recognized with an SSH (sea surface height) method; step two, for a deformation control based similarity match method, the eddies in the range and attributes of the eddies are subjected to similarity calculation of area, amplitude, kinetic energy, relative vorticity and Hausdorff distance, the eddy with the maximum similarity is selected as the position of the next eddy, and jump of an eddy path is avoided through combination of physical attributes and geometric attributes of the eddies; step three, the delay logic is adopted, search at multiple time points is considered, the eddies temporarily disappearing at certain time points are processed, and discontinuity of the eddy path is avoided, so that the purpose of multi-year long-term efficient tracing on the eddies is achieved.