The interaction between ε-polylysine (ε-PL) and anionic polysaccharides has gained considerable attention recently because of its scientific impact on the stability and appearance of liquid food systems. The purpose of this study was to characterize the interactions between ε-PL and carboxymethyl sweet potato starch (CSS) using isothermal titration calorimetry (ITC), electrical charge, and turbidity measurements. The results showed that the interaction between ε-PL and CSS was electrostatic and mainly dependent on the molar ratio of amino groups in ε-PL to carboxyl groups in CSS. Additionally, the interaction between ε-PL and CSS was also associated with pH, degree of substitution (DS) of CSS, and ionic strength of the system. For the interaction of ε-PL with high DS (>0.235) CSS, three states of the ε-PL/CSS mixture were observed as transparent, turbid, and precipitated with a successive increase in amino/carboxyl molar ratio. Distinguishingly, a transparent mixture could be obtained for CSS with low DS (0.114) at a sufficiently high amino/carboxyl molar ratio. The present study provided basic guidance in designing liquid food systems containing both ε-PL and CSS.