Multidrug-resistant bacterial infections have become an important cause of clinical death in the twenty-first century. Much effort has been made to overcome this challenge. The discovery of novel antimicrobial compounds, as well as the rational use of antibacterial drugs with different structure types and mechanisms, is helping to deal with bacterial resistance. Currently, pyrimidine-containing agents are the major areas of new antibacterial drug discovery. Given their good activities and diverse mechanisms of action, many pyrimidine-containing heterocyclic compounds have become the focus of interest for many scientists. In addition, pyrimidine structure is an important part of many endogenous substances, which is an advantage that allows pyrimidine derivatives to interact with genetic materials, enzymes and other biopolymeric substances in the cell. Scientists have focused on the discovery and structural optimization of pyrimidine derivatives, which has resulted in the discovery of many novel pyrimidine derivatives with intriguing profiles. Herein we summarize the therapeutic potentials of pyrimidine compounds that are promising for antimicrobial applications over the last decade. In particular, the relationships between the structures of modified pyrimidines and their antimicrobial activity are systematically discussed.