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The synergistic antibacterial effects of lotus seedpod oligomeric procyanidins (LSPC) and water-soluble Poria cocos polysaccharides (WPCP) against two Escherichia coli (E. coli) strains were evaluated. The mixture showed an obviously synergistic inhibitory effect against E. coli, improving the adverse effects by which LSPC at low concentration (≤0.8 mg/mL) proliferated E. coli. The minimal inhibitory concentration (MIC) of the mixture was significantly lower compared with LSPC alone against E. coli strains. The main mechanism of LSPC and the mixture against E. coli strains caused damage of cell membranes and increased the intracellular oxidative stress. The changes in the FT-IR and UV–vis spectra showed that there was interaction between LSPC and WPCP, and the changes of zeta potential of different samples might offer possible reasons for its improved antibacterial activity. Moreover, the results demonstrated that the mixture had more potential than LSPC for natural bacteriostatic agents and probiotics.