The heavy metal sources of large-scale raceway pond microalgae cultivation with flue gas were investigated to reduce heavy metal contents in microalgae during cultivation. The microalgae were cultivated with power plant flue gas (as C source) and circulating cooling seawater (added with N and P nutrients) for 6 days. The Pb, Cd, Hg, and As contents in microalgae were 0.91, 0.22, 0.08, and 0.28 ppm, respectively, which are nearly within the available national standard for food-grade microalgae. The heavy metal contents in microalgae with two membrane materials, namely, elastic polyethylene and random copolymer polypropylene, barely increased. The Hg, As, and Pb contents in microalgae cells cultivated with pure CO2 were 16.67%, 69.23%, and 70.33% that of cells cultivated with CO2 from flue gas. The Pb, As, and Hg contents in cells cultivated with fresh water were reduced by 38.46%, 15.38%, and 37.50%, respectively, compared with those cultivated with seawater. The heavy metal contents in microalgae were further reduced and controlled.