Heavy metal wastewater often contains multiple metal ions, and competition among them reduces the adsorption efficiency of microalgae. Enhancing this efficiency is crucial for improving heavy metal removal. This study optimized lysine addition to facilitating the formation of a ternary complex between microalgae, lysine, and heavy metals, thereby enhancing adsorption in both single- and mixed-metal systems. In a single-metal system at 64 mg/L, lysine improved the removal rates of copper, zinc, and cadmium by 13.96%, 41.21%, and 33.26%, respectively. In binary systems (Cu-Zn, Cu-Cd, and Cu-Pb) at 32 mg/L, lysine increased copper adsorption by 11.81%, 15.71%, and 25.25%, while improving zinc, cadmium, and lead adsorption by 15.41%, 12.51%, and 3.93%, respectively. Competitive adsorption analysis revealed that lead most strongly inhibited copper adsorption, while copper significantly suppressed zinc adsorption. Mechanistic investigations using 3D-EEM, FTIR, and XPS demonstrated that humic substances in the extracellular polymeric substances (EPSs) of microalgae play a key role in lysine binding. This interaction increases the number of carboxyl functional groups on the cell surface, thereby enhancing the microalgae’s capacity to adsorb heavy metals.