The present invention relates to the technical field of molecular marking and particularly relates to common camellia oleifera SSR molecular marker primers and a marking method and an application thereof. The common camellia oleifera roots are subjected to RNA extraction, sequencing and assembly, MISA is used to search SSR sites, corresponding primers are designed, camellia oleifera genome DNA isused as a material, the designed SSR primers are validated, and the corresponding primers are obtained from the designed 6,738 pairs of the primers. The primers show polymorphism, can successfully distinguish the camellia oleifera materials of different varieties, provide the new molecular markers for molecular marking auxiliary breeding of the camellia oleifera, and provide new ideas for future researches on genetic breeding, genome mapping, gene mapping, species genetic relationship identification, etc.