The comparative molecular similarity index analysis (CoMSIA) model of double-activity quinolones targeting green algae toxicity and bacterial genotoxicity (8:2) was constructed in this paper on the basis of the comprehensive index method. The contour maps of the model were analyzed for molecular modifications with high toxicities. In the CoMSIA model, the optimum number of components n
was 7, the cross-validated q2
value was 0.58 (>0.5), the standard deviation standard error of estimate (SEE) was 0.02 (<0.95), F
was 1265.33, and the non-cross-validated R2
value was 1 (>0.9), indicating that the model had a good fit and predicting ability. The scrambling stability test parameters Q2
, cross-validated standard error of prediction (cSDEP), and dq2
yy were 0.54, 0.25, and 0.8 (<1.2), respectively, indicating that the model had good stability. The external verification coefficient r2pred
was 0.73 (>0.6), and standard error of prediction (SEP) was 0.17, indicating that the model had a good external prediction ability. The contribution rates of the steric fields, electrostatic fields, hydrophobic fields, hydrogen bond donor, and acceptor fields were 10.9%, 19.8%, 32.7%, 13.8%, and 22.8%, respectively. Large volume groups were selected for modification of ciprofloxacin (CIP), and the derivatives with increased double-activity characterization values were screened; the increase ratio ranged from 12.31–19.09%. The frequency of derivatives were positive and total energy, bioaccumulation, and environmental persistence was reduced, indicating that the CIP derivatives had good environmental stability and friendliness. Predicted values and CoMSIA model constructed of single activities showed that the CoMSIA model of double activities had accuracy and reliability. In addition, the total scores of the derivatives docking with the D1 protein, ferredoxin-NADP (H) reductases (FNRs), and DNA gyrase increased, indicating that derivatives can be toxic to green algae by affecting the photosynthesis of green algae. The mechanism behind the bactericidal effect was also explained from a molecular perspective.