In this study, the joint toxicological characteristics of reproductive toxicity, neurotoxicity, and endocrine disruption (ED) by organophosphorus flame retardants (OPFRs) were regulated by process control. Molecular docking technology, molecular dynamics (MD), 2D-QSAR model, and density functional theory (DFT) were used to develop a health risk regulation scheme for special population such as pregnant women exposed to OPFRs. It was found that MD simulations confirmed the effectiveness of the recommended complementary food scheme (CFS) for the pregnant women with low health risk. When β-lactoglobulin, α-lactoalbumin, milk fat globule membrane (MFGM) protein, ovalbumin (OVA), ovotransferrin (OVT), vitamin, plant pigment, apple polyphenols, and malic acid were present in the CFS, the joint toxicity of OPFRs in pregnant women were significantly decreased by 91.18%. The reproductive toxicity played a dominant role in the joint toxicity and could be reduced by 82.48% under the recommended CFS. There was a competitive relationship between the nutrients in the recommended CFS and OPFRs binding to the joint toxic receptor (JTR). The former could easily occupy the target binding spot of the JTR protein, which reduced or prevented the binding of OPFRs to the JTR. In addition, simulation of OPFRs molecular metabolic pathways in pregnant women under the recommended CFS showed that the binding affinity between OPFRs and six metabolic kinases in pregnant women was significantly decreased (–28.85% -–87.54%), indicating that the inhibition effect of OPFRs on normal biochemical reactions in the human body was significantly reduced, which to a certain extent verified the effectiveness of the recommended CFS.