The continuous cropping of Glycyrrhiza glabra L. caused the decline of G. glabra yield, poor plant development and frequent root rot, which seriously affected the development of G. glabra industry and caused serious economic losses. However, their mechanisms were unknown. The 16S rDNA and 18S rDNA internal transcribed spacer sequences of soil without plant cover (Control) and rhizosphere soil of 1- (Gg1) and 5-year-old G. glabra (Gg5) in fields were determined by next generation sequencing technology. Differences in microbial community structures among the three soil types were analyzed to explain obstacles associated with continuous G. glabra cropping. The results show that monoculture of G. glabra respectively increased and reduced bacterial and fungal community richness in rhizosphere soil over time (P>0.05). Principal co-ordinates analysis illustrated that there were obvious differences between the rhizosphere soil microbial composition of G. glabra and the control group, and the planting years of G. glabra observably affected the microbial community composition in rhizosphere soil. At the phyla level, monoculture of G. glabra observably enhanced the relative abundance of Blastocladiomycota and Mortierellomycota. At the genus level, monoculture of G. glabra observably decreased the relative abundance of beneficial microbes Arthrobacter, Pseudomonas and Naganishia, and enhanced the relative abundance of pathogenic fungi Fusarium and Thanatophorus. Therefore, variances in the microbial community structures in the rhizosphere soil of G. glabra, especially the respectively decreased and increased beneficial and pathogenic microbes, might explain obstacles with continuously cropped G. glabra.