Fluoroquinolone antibiotics (FQs), one of the most widely used antibacterials, have been recognized as emerging contaminants with adverse human health concerns. To overcome the adverse effects, a theoretical molecular design and screening approach was developed in this study to improve the removal efficiency of FQs by Chlorella in artificial or natural wetland systems. Among the 189 designed norfloxacin (NOR) derivatives, NOR-140 was screened with significantly improved biosorption, bioaccumulation, and biodegradation removal and functional effects, and reduced human health and ecological risks. The removal mechanism NOR-140 was also analyzed using adsorption kinetics, molecular docking, molecular dynamics simulations and machine learning models. Protein and polysaccharide structures play a major role in the adsorption process, polarizability and molecular volume of NOR-140 affect the bioaccumulation ability, and hydrogen bonding was found as the key force promoting the degradation ability of NOR-140. Modifying specific sites (5, 8, and 13) with functional groups containing highly electronegative atoms (O, F) significantly enhances the biodegradability of FQs alternatives by Chlorella. This study provided theoretical support for designing environmentally friendly FQs alternatives with improved degradation ability and advanced the understanding of how the FQs' molecular structures affect its removal by Chlorella.