A previous study demonstrated that Weissella confusa SJ-5, a strain isolated from sweet potato sour liquid during starch production, could efficiently flocculate sweet-potato starch, yet the underlying molecular mechanism and structural basis remained unclear. In this study, the bacterial surface was selectively enzymatically treated, and a combination of Fourier-transform infrared spectroscopy, Zeta-potential analysis, and bond-blocking assays was employed to elucidate the starch-flocculation mechanism of W. confusa SJ-5. Effect of pH and ionic strength on flocculation efficiency was also investigated. The results suggested that flocculation of starch by W. confusa SJ-5 was greatly influenced by surface protein, lipids, and extracellular polysaccharides. Heat-shock protein 70 (Hsp70) and the chaperonin GroEL were identified as the key surface proteins responsible for starch-bonding. Interactions between the bacterium and starch were primarily mediated by ionic bonds, in accordance with the bridging-adsorption mechanism. Both pH and ion concentration significantly modulated flocculation performance. The flocculation rate initially increased and subsequently declined as pH or ionic strength rose, peaking at 69% under the optimized conditions of pH8.0 and 20 mmol/L K⁺. These findings provide a theoretical basis for the application of W. confusa SJ-5 as a low-cost biological flocculant in starch production.