Fluoroquinolone antibiotics (FQs) have been used worldwide due to their extended antimicrobial spectrum. However, the overuse of FQs leads to frequent detection in the environment and cannot be efficiently removed. Microalgae-based constructed wetland systems have been proven to be a relatively proper method to treat FQs, mainly by microalgae, plants, microorganisms, and sediments. To improve the removal efficiency of microalgae-constructed wetland, a systematic molecular design, screening, functional, and risk evaluation method was developed using three-dimensional quantitative structure–activity relationship models, molecular dynamics simulation, molecular docking, and TOPKAT approaches. Five designed ciprofloxacin alternatives with improved bactericidal effects and lower human health risks were found to be more easily degraded by microalgae (16.11–167.88 %), plants (6.72–58.86 %), microorganisms (9.10–15.02 %), and sediments (435.83 %–1763.51 %) compared with ciprofloxacin. According to the mechanism analysis, the removal effect of the FQs can be affected via changes in the number, bond energy, and molecular descriptors of favorable and unfavorable amino acids. To the best of our knowledge, this is the first comprehensive study of improving the microalgae, plants, microorganisms, and sediment removal efficiency of FQs in constructed wetlands, which provides theoretical support for the treatment of FQ pollution.