The German cockroach, Blattella germanica (L.) (Blattaria: Blattidae) harbored diverse microorganisms in the digestive tract, including bacteria, fungi, viruses, archaea, and protozoa. This diverse community maintains a relatively stable balance. Some bacteria have been confirmed to play crucial roles in the insect's physiology, biochemistry, and behavior. Antibiotics can effectively eliminate bacteria and disrupt the balance of gut microbiota, but the time-course of this process, the structure of the new microbial community, and the dynamics of re-assemblage of a bacterial community after antibiotic treatment have not been investigated. In the present study, antibiotic (levofloxacin and gentamicin) ingestion reduced bacterial diversity and abundance in the cockroach gut. Within 14 d of discontinuing antibiotic treatment, the number of culturable gut bacteria returned to its original level. However, the composition of the new bacterial community with greater abundance of antibiotic-resistant Enterococcus and Dysgonomonas was significantly different from the original community. Network analysis showed that antibiotic treatment made the interaction between bacteria and fungi closer and stronger in the cockroach gut during the recovery of gut microorganisms. The study on the composition change, recovery rules, and interaction dynamics between gut bacteria and fungi after antibiotic treatment are helpful to explore gut microbes' colonization and interaction with insects, which contributes to the selection of stable core gut bacteria as biological carriers of paratransgenesis for controlling Blattella germanica.