Molecular docking, molecular dynamics modelling, and fractional factorial design methodologies were used in the current work to examine the harmful effects of ten microplastic (MPs) such as polystyrene (PS), polyvinylchloride (PVC), polyurethane (PU), polymethyl methacrylate (PMMA), polyamide (PA), polyethylene terephthalate (PET), polyethylene (PE), polypropylene (PP), polychloropene (PCP) and polycarbonate (PC) on the aquatic organism (zebrafish). The toxicity was evaluated based on the docking of the MPs on cytochrome P450 (CYP P450) protein crystals. The binding affinities (ΔG) followed the order, PC (−6.9 kcal/mol) > PET (−6.1 kcal/mol) > PP (−5.8 kcal/mol) > PA (−5.6 kcal/mol) > PS (−5.1 kcal/mol) > PU (−4.1 kcal/mol) > PMMA (−3.9 kcal/mol) > PCP (−3.3 kcal/mol) > PVC (−2.4 kcal/mol) > PE (−2.1 kcal/mol). The primary driving factors for the binding of the MPs and the protein were hydrophobic force, and hydrogen bonding based on the molecular dynamics analysis and surrounding amino acid residues. Furthermore, a 210−5 fractional factorial design method was estimated to identify the main effect and second-order effects of MPs in a composite contamination system on binding affinity/energy to CYP450 receptor protein of zebrafish, combined with a fixed effects model. The findings showed that different MPs combinations had varying impacts on aquatic toxicity; as a consequence, the best combination of MPs with the lowest aquatic toxicity effect could be excluded. The factorial designs showed that the PU-PS and PP-PA combination and single PCP, has the most significant main effect on CYP450 receptor protein of zebrafish which translates to an optimum toxicity level of −4.61 kcal/mol. The investigation offers a theoretical foundation for identifying the hazardous impacts of MPs on aquatic life. Display omitted •Polycarbonate have high binding affinity on CYP P450 protein crystals.•The hydrophobic force, and hydrogen bonding are primary driving factors for the binding of the MPs and the protein.•A 210−5 fractional factorial design method was estimated to identify the main effect.•PU-PS and PP-PA combination and single PCP, has the most significant main effect on zebrafish.