Microbiome associated with insects play vital roles in host ecology and physiology. The small brown planthopper (SBPH), Laodelphax striatellus, is a polyphagous insect pest that caused enormous damage to a wide range of cereal crops. Previous studies have assessed the effects of environmental factors, such as antibiotics, insecticide, and geographical habitat on the bacterial composition of SBPH. However, the influence of host plants on the microbial community in SBPH still unclear. Here, we characterized and compared the microbial community in three SBPH populations feeding on rice, barley, and wheat, respectively, using high-throughput amplicon sequencing. Our observations revealed that the microbiome harbored by SBPH was abundant and diverse. Ten phyla comprising 141 genera of bacteria were annotated, and four fungal phyla consisting of 47 genera were assigned. The bacteria belonging to the phylum Proteobacteria were the most prevalent and the fungi with the highest abundance were from the order Hypocreales. Comparative analysis showed that host plants could significantly induce structural changes of SBPH microbiome. Significant differences in abundance were observed in two main bacterial orders (Rickettsiales and Rhodospirillales) and three fungal classes (Sordariomycetes, an unclassified class in Ascomycota and Eurotiomycetes) among three host-adapted SBPH populations. Our results could broaden our understanding of interactions among SBPH, its microbial associates and host plants, and also represented the basis of future SBPH biological management.