At present, the assessment of photooxidation system mainly focuses on the photodegradation efficiency of target pollutant, lacking of the toxicity assessment in the photocatalysis process. Here,photodecomposition of bisphenol A (BPA) was used to investigate the performance of several cyclodextrin modified photocatalysts. Moreover, the comprehensive toxicity changes of BPA under different photocatalytic oxidation conditions were conducted. The β-cyclodextrin (β-CD) modified photocatalyst, including titanium dioxide (CM-β-CD-TiO2), carbon nitride (CM-β-CD-C3N4) and cadmium sulfide (SH-β-CD-AM/CdS) exhibit high degradation rate and mineralization efficiency of BPA. The highest total organic carbon (TOC) removal of BPA observed in the oxidation system of SH-β-CD-AM/CdS nanoreactor (73.4％). The main oxidation intermediates in these systems were detected, and the comprehension toxicity of BPA and its oxidation intermediates in different system were compared by toxicity estimation software tool (T.E.S.T.) based on quantitative structure-activity relationship (QSAR) prediction. The results show that β-CD can facilitate the photodecomposition of the target contaminant.However, many oxidation intermediates with high comprehensive toxicity, even in the oxidation system with high BPA removal, can still be detected. Therefore, not only decomposition of target contaminant but also the comprehensive toxicity of oxidation intermediates should be regarded as index to evaluate a photocatalysis technology.