Novel 3D-printed buoyant structures can be applied in various environmental processes because of their considerable advantages. Microalgae cultivation in photobioreactors, directly supplemented by industrial CO2, enables environmental pollution mitigation/cleanup and sustainable energy production. However, in photobioreactor systems, biofilm formation due to gas bubbling decreases microalgal productivity. Therefore, in this study, we aimed to develop a novel 3D-printed buoyant structure to suppress biofilm formation. The 10 mm-sized spherical buoyant structure reduced the height and area of the biofilm by 58.3% and 82.5%, respectively. The structure decreased space where bubble burst occurred and controlled the bubble size, reducing the overall biomass loss by 58.7%. It did not reduce photobioreactor performance noticeably during semi-continuous cultivation, indicating the possibility of long-term applicability. In large-scale outdoor microalgae cultivation using flue gas CO2, the buoyant structure improved the cell density and biodiesel production potential without contamination. This study provides a promising strategy to contribute to biological CO2 mitigation through the utilization of flue gas CO2 for enhanced microalgal production, paving the way for energy and environmental sustainability.