Symbiotic microbiomes play important roles in hosts’ adaptation and evolution. Here, the gut bacterial communities in Cephalcia chuxiongica, a key pest of pines in China, were studied for the first time by using 16S rRNA amplicon sequencing. The composition of gut bacterial communities differed in different C. chuxiongica geographic populations, while the various microbes performed similar functions, suggesting some kinds of functional complementation. The predicted functional profiles of microbes indicated that most of identified KEGG Pathways were shared by different populations, in which metabolism was the most dominant functional pathway. Moreover, the function of major microbes associated with host dietary specialization (pine needles), such as cellulose degradation. All samples contained abundant Wolbachia, which may play important roles on the parthenogenesis of C. chuxiongica. The high abundances of Serratia and Sphingomonas in samples suggest that gut microbiota may crucial for the long-term larval diapause in C. chuxiongica. Interestingly, this study found that the phylogeny and diversity of gut microbiota correlated to host geographic/genetic distance, i.e., the microbiota was more similar as the geographic/genetic distance decreased, and vice versa. Therefore, the synergy of environmental and host factors appears to be the main force shaping the structure and variability of gut microbiota and likewise, gut microbiota may exert a significant effect on its host by shaping host biological characters, suggesting some kinds of extraordinary symbiosis and coevolution. These results demonstrate the important contribution of gut microbiota and provide a sound foundation for developing control strategies for this pest.