Honeybee is an important pollinator for maintaining ecological balance. However, scientist found the bizarre mass death of bees in winter. Meanwhile, some reported that the differences composed of intestinal bacteria between healthy honeybees and CCD honeybees. It is essential that explored dynamic changes to the intestinal bacteria in overwintering honeybees. We collected bee samples before overwintering, during prophase of overwintering, metaphase of overwintering, anaphase of overwintering, telophase of overwintering, and after overwintering. By using high-throughput sequencing targeting the V3−V4 regions of the 16S rDNA, the abundance of the intestinal bacteria were analyzed in overwintering honeybees. A total of 1,373,886 high-quality sequences were acquired and Proteobacteria (85.69%), Firmicutes (10.40%), Actinobacteria (3.66%), and Cyanobacteria (1.87%) were identified as major components of the intestinal bacteria. All core honeybee intestinal bacteria genera, such as Gilliamella, Bartonella, Snodgrassella, Lactobacillus, Frischella, Commensalibacter, and Bifidobacterium were detected. The abundance of Actinobacteria, Bartonella, and Bifidobacterium increased initially and then decreased in winter honeybees. There were no significant differences in the richness and evenness of the microbiota in overwintering honeybees; however, there was a statistically significant difference in the beta diversity of the intestinal bacteria after overwintering compared with that in other groups. Our results suggested that honeybees maintained their intestinal ecosystem balance, and increased the abundance of gut probiotics in response to environmental and nutrition pressures in winter.