Foam flotation is generally recognized as a low-cost and efficient technology for the harvesting of microalgae for food, feed and fuel production, as well as environmental remediation. However, the harvesting efficiency of microalgae using foam flotation is restricted by the residual metal cations in the medium, and the corresponding inhibition mechanism has not yet been revealed. This study investigated the effects of metal cations in the medium on the harvesting efficiency and concentration factor during the foam flotation of Scenedesmus acuminatus. The interface interaction of cell-collector-bubble effected by metal cations was revealed by quantifying the amount of collector (cetyl trimethylammonium bromide, CTAB) between cells and bubbles, as well as the response of bubble interface characteristics. Results showed that the harvesting efficiency dropped linearly as the increase of cationic concentrations. Under the CTAB dose of 20 mg L−1, the harvesting efficiency decreased from 98.65% to 56.77% with a decrease of concentration factor from 25.41 to 9.05 in the presence of metal cations. The Na+ and Mg2+ in the medium were the major inhibitors. The inhibitory mechanisms revealed that metal cations obviously impeded the adsorption of CTAB onto the cells by competing adsorption site, resulting in a low harvesting efficiency. The presence of metal cations also inhibited the bubble coalescence and slowed down drainage velocity in the plateau channel of foam layer, forming foam with higher water content, thus reducing the concentration factor. A schematic illustration is proposed to better understand the effect mechanism of metal cations on microalgal foam flotation. This study might facilitate the process development in an effort to overcome the inhibition of cations during microalgal foam flotation.