The synthesis, antibacterial activity and mechanism of Yb³⁺-Catechin complex (Yb³⁺-C) were systematically studied in this work. The experimental results showed that the optimum coordination mole ratio of Yb³⁺-C was 1∶4. The minimum inhibitory concentration (MIC) of Yb³⁺-C was significantly lower than that of single Yb³⁺ and C. Yb³⁺-C exhibited high antibacterial activity against Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa and Salmonella, and more effective for Staphylococcus aureus and the MIC value was only 0.0963 mmol/L. Further investigation showed that the sterilization time of Yb³⁺-C was greatly reduced to 2 h. In addition, the analysis of scanning electron micrograph (SEM), transmission electron microscope (TEM), and adsorption and distribution of Yb³⁺ in cell membranes and intracellular indicated the stronger affinity and penetration ability of Yb³⁺-C to bacterial cells. Therefore, the Yb³⁺ in the form of Yb³⁺-C is more easily accumulated to the effective concentration in the cytoplasm, resulting the damage of cellular structure and apoptosis.