Panax notoginseng has long been used as a Chinese herb with high medicinal value. The endophytic bacteria in this medicinal plant have multiple biological functions. High-throughput sequencing is a rapidly evolving technique that helps profile the endophytic bacterial community structure of medicinal plants. However, few studies on the endophytic bacteria in P. notoginseng, particularly in dry P. notoginseng roots as a raw medicinal material, have been conducted. In this study, fresh P. notoginseng and dry P. notoginseng were analysed using high-throughput sequencing on an Illumina MiSeq platform to explore the diversity and functions of the endophytic bacteria in different parts of P. notoginseng. The results showed that a total of 201 operational taxonomic units were obtained from fresh P. notoginseng and dry P. notoginseng. The dominant phyla in the fresh and dry P. notoginseng were Proteobacteria (85.9%) and Firmicutes (99.9%), respectively, whereas the dominant genera in these samples were Enterobacter (84.4%) and Bacillus (99.6%), respectively. Fresh P. notoginseng exhibited a higher degree of endophytic bacterial diversity than dry P. notoginseng, but functional prediction of metabolism indicated that the relative abundance of the metabolic function of terpenoids and polyketides synthesis in the dry sample was higher than that in the fresh sample. Our study indicates significant differences in the diversity and metabolic function of the endophytic bacteria between fresh and dry P. notoginseng, providing useful information for the exploitation and utilization of endophytic bacteria resources from P. notoginseng.