Reducing post-acidification is crucial for extending the shelf-life and facilitating industrial-scale production of low-salt paocai. This study aimed to screen and identify a lactic acid bacteria strain with weak post-acidification potential from 39 commonly used strains in vegetable fermentation. We employed transcriptomic and metabolite analysis to investigate the mechanisms underlying the weak post-acidification traits of the selected strain. Notably, W. cibaria SC5R3 had a minimum survival rate at pH 4.5 by 39.02% and survival rate to pH 4.0 was only 1.82%. The incorporation of W. cibaria SC5R3 in low-salt paocai showed a low content of total titratable acidity and stable viable count during 8 days of storage at 25°C, which also exhibited good sensory quality. Furthermore, W. cibaria SC5R3 exhibited significant down-regulation of genes associated with the hetero-fermentation pathway during late-stage fermentation, contributing to its weak acid-producing characteristic. The strain SC5R3 displayed deficiencies in the glutamate decarboxylase system, histidine synthesis, and aspartate metabolism, along with reduced H⁺-ATPase activity in acidic environments, making it sensitive to acid. This research provides valuable insights into optimizing low-salt paocai fermentation processes and improving product quality by minimizing acidity changes during shelf-life storage.