Microalgae are a sustainable environmentally friendly wastewater treatment technology that has attracted much attention for use in the purification of antibiotic-containing wastewater. However, research into the mechanisms involved in microalgal antibiotic degradation is still in the initial stages, especially concerning the relationship between pollutant structure and removal rate. This study comprehensively analyzed the antibiotic biodegradation mechanisms in microalgae from a molecular structure perspective, examining four sulfonamide antibiotics (SAs) with different substituents as representative pollutants. Microalgae exhibited removal efficiencies of 86.15, 74.24, 60.14, and 46.60% for sulfathiazole, sulfamethazine, sulfadiazine, and sulfamethoxazole, respectively. It is noteworthy that cytochrome p450 (CYP450) played a central catalyzing role in their metabolism. Further analysis of molecular dynamics simulations and density functional theory calculations revealed that the geometric differences and electronic effect variations caused by the substituents significantly affected the catalytic activity of CYP450 as well as the overall reactivity of the SAs, resulting in different removal rates. Overall, SAs with high binding energy, low energy gap, and high electrophilicity indices were more readily catalyzed by CYP450 as evidenced by the degradation pathways. These results provide valuable insights at the molecular level into how different substituents affect the degradation rate of SAs in microalgae.