A named entity marking apparatus, a named entity marking method, and a computer program product thereof are provided. The named entity marking apparatus comprises a processor and a storage unit, wherein the processor is electrically connected to the storage unit. The storage unit is stored with an electronic document and a named entity database. The processor marks the electronic document into a first marked document by a first set of the named entity database. The processor decides a second set of the named entity database according to the first marked document. The processor re-marks the electronic document into a second marked document by the second set of the named entity database.