As a kind of additive flame retardant, polybrominated biphenyls (PBBs) will be released from the product slowly and enriched in environmental media and organisms to cause harm. Infrared and ultraviolet spectra can detect PBBs, which have the advantages of rapid detection, no secondary pollution and simple operation, etc. In this paper, the efficacy coefficient method was used to synthesize the two spectral effects of infrared vibration and ultraviolet absorption of PBBs and a CoMFA model with dual spectral effects was established. PBB-153 Derivatives with increased infrared and ultraviolet spectral intensity are designed according to the contour maps of the model. The stability, functionality and environmentally friendliness of derivatives were evaluated. The results showed that the main component n of the CoMFA model is 3, and the cross-validation coefficient q² was 0.532 (>0.5), indicating that the model has a good prediction ability; SEE was 0.013 (<0.95), F was 38.281, and non-cross-validation coefficient R² was 0.935 (>0.9), which indicates that the model has the good fitting ability; the scrambling stability test parameters Q², cSDEP and dq²/dr²yy were 0.51, 0.04, and 0.95 (<1.2), respectively, the model has good robustness. External verification was constructed through the test set, SEP was 0.03, rpred2was 0.73 (>0.6), indicating that the model has a good external prediction ability, and the steric and electrostatic field’s contribution rates are 44.8% and 55.2%, respectively. According to the contour maps’ information of the model, 7 PBB-153 derivatives were designed, the change rates of comprehensive values of the dual spectral increased ranged 10.15%~29.12%. The Gaussian calculation results showed that the Gibbs free energy value of the derivative was less than 0 and the frequency was greater than 0. The C-Br bond dissociation enthalpy changeds lightly, indicating that the derivatives have good environmental stability and function. In addition, the environmental persistence, long-distance transmission, toxicity and bioenrichment of all derivatives were reduced, and the environmental friendliness was improved. Model validation results showed that the derivatives’ single effects of infrared and ultraviolet were rising, and two spectral intensities changed the ratio of derivative No.4 (4-OCN-5-NO-PBB-153) was 0.79, close to the set proportion of 1∶1, and the contour maps of dual effects basically contained the information of that of the single spectra effects model, indicating that the established CoMFA model has a certain accuracy and reliability. The established CoMFA model can accomplish the modification and comprehensive analysis of two single spectral effects simultaneously, providing the idea for the comprehensive evaluation of the spectral detection of other pollutants.