The invention relates to a global nearest neighbor method-based method and system for merging trace points between beam positions. The method comprises the following steps of (S1) carrying out interior trace point merging processing on obtained trace points in single beam positions; (S2) carrying out similarity measurement and calculation on the trace points at two adjacent beam positions to obtain a distribution cost matrix; (S3) carrying out global solution calculation on the distribution cost matrix and judging associated trace point pairs; and (S4) merging the associated trace points into one trace point, adding the trace point to a condensation trace point table and directly adding all trace points except for the associated trace points to the condensation trace point table. The invention further provides a system. The system comprises a single-beam position trace point processing module, a similarity measurement and calculation module, a distribution cost matrix calculation module and a trace point merging processing module. Global nearest neighbor association is carried out on the trace points between the beam positions, so that the trace point merging efficiency of the system can be improved, and meanwhile, the accurate rate of merging the trace points between the beam positions is improved.