Background: Klebsiella pneumoniae is an important opportunistic pathogen and zoonotic pathogen. The widespread use of antibiotics has led to the emergence of a large number of multidrug-resistant Klebsiella pneumoniae in clinical animal husbandry, posing a serious threat to global health security. Protocatechuic acid (PCA) is a phenolic acid substance naturally present in many vegetables and fruits. It is a safe and highly developed new type of antibacterial synergist. Purpose: This study explored the antibacterial and synergistic mechanisms of PCA against Carbapenem-resistant hypervirulent Klebsiella pneumoniae. Study design: Metabolomic analysis using PCA to investigate the metabolic effects of CR-hvKP and further explore the antibacterial mechanisms resulting from this metabolic regulation. Methods: The MIC of PCA was measured by microdilution, and its bactericidal effect was observed by DAPI staining. Resistance and hemolysis tests were performed to ensure safety. The synergy of PCA and meropenem was tested by checkerboard assay. The biofilm inhibition was assessed by crystal violet and EPS assays. The membrane morphology, permeability, and potential were examined by SEM, PI, NPN, and DiSC3(5). The metabolic changes were evaluated by AlamarBlue, metabolomics, enzyme activity, ELISA, molecular docking, and qRT-PCR. The oxidative stress and metabolic disorders were verified by NADP(H), ROS, MDA, and ATP assays. Results: The results showed that PCA can synergize with antibiotics and inhibit the biofilm and membrane functions of CR-hvKP at low concentrations. Metabolomics revealed that PCA affects the EMP and PPP pathways of CR-hvKP, causing oxidative stress. This involves the binding of PGAM and the downregulation of BPGM, leading to the accumulation of glycerate-3P. This results in the inhibition of G6PDH and the imbalance of NADPH/NADP+, disrupting the energy metabolism and increasing the oxidative stress, which impair the biofilm and membrane functions and enhance the antibiotic efficacy. Conclusion: The results demonstrate that PCA regulates the EMP-linked PPP pathway of CR-hvKP, inhibits biofilm and membrane functions, and synergizes with antibiotics to kill bacteria, providing new insights and candidates for natural antibacterial enhancers.