Non-invasive laser irradiation can induce photobiomodulation of cells and tissues. Photobiomodulation (PBM) is widely used, especially in antimicrobial infection and improving inflammation. However, studies have found that PBM has a bidirectional regulation of bacteria and inflammation. Antibacterial and pro-bacterial, anti-inflammatory and pro-inflammatory will change under different experimental conditions. In recent years, the clinical applications of PBM have received more and more attentions, especially in the field of antibacterial, because it is a noninvasive strategy with few contraindications. However, due to the bidirectional regulatory effect, researchers still have doubts about the application mode of PBM, and the parameters such as light wavelength and dose must be modified according to its clinical application. Therefore, this paper summarizes the bidirectional regulation effects of PBM on bacteria, and analyzes the influencing factors and molecular mechanism of this bidirectional regulation effect. The bidirectional regulation effect of PBM on bacteria is affected by light wavelength, dose, bacterial category and bacterial state. A better understanding of the degree of bidirectional dose-response in low-intensity laser therapy is necessary to optimize clinical treatment. It can also help explore the most reliable mechanism of PBM use and ultimately standardize the treatment of patients with various diseases. In addition, rational use of the bidirectional regulation mechanism of PBM can promote or inhibit the growth of bacteria, which has broad application prospects in the fields of microbial manufacturing, flora regulation, improvement and treatment of diseases.