Background This study aimed to improve the sustained and controlled release of glycyrrhizic acid to the infected site of Staphylococcus aureus small colony variants (SCVs). Methods The glycyrrhizic acid-loaded chitosan composite nanogel was prepared by inclusion action, Schiff's base formation, and electrostatic action. Furthermore, the formulation screening, characteristics, in vitro release, and antibacterial activity of the glycyrrhizic acid composite nanogel were explored. Results The final optimal formula comprised 10 mg/mL (chitosan) and 50 μL (glutaraldehyde). The loading capacity, encapsulation efficiency, mean size, polydispersity index, and zeta potential were 8.8%±1.6%, 92.1%±2.8%, 478.3±2.8 nm, 0.37±0.10, and 25.3±3.6 mv, respectively. Scanning electron microscope images showed a spherical shape with a relatively uniform distribution. The in vitro release study showed that glycyrrhizic acid composite nanogel exhibited a biphasic pattern with a sustained release of 52.1%±2.0% at 48 h in the pH 5.5 PBS. The minimum inhibitory and minimum biofilm inhibitory concentrations of glycyrrhizic acid composite nanogel against SCVs were 0.625 μg/mL. The time-killing curves and live/dead bacterial staining showed that glycyrrhizic acid composite nanogel had a stronger curative effect against SCVs strain with concentration-dependent. Conclusion This study provides promising glycyrrhizic acid composite nanogel to improve the treatment of SCV infection.