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Refractory pollutants often exist in wastewater after photocatalysis. Here, experiments, gas chromatography-mass spectrometry (GC–MS) analysis and density functional theory (DFT) simulations were used to explain the different levels of photocatalytic degradation of organics in papermaking wastewater associated with two photocatalytic processes with the goal of improving environmental sustainability. The photocatalytic experiments of flocculation and SBR effluents of papermaking wastewater were studied in a reactor with nano-TiO2 colloid, followed by GC–MS analysis, and the different degradation levels of organics were explained based on DFT adsorption and photocatalysis simulations. The experimental results show that the total COD removal rates were 65.8% and 90.8% for the flocculation-photocatalysis and SBR-photocatalysis processes, and the resin acids and fatty acids in wastewater were classified as easily degradable pollutants and esters as refractory pollutants. The adsorption and photocatalysis simulations show that compared with dehydroabietic acid and pentadecanoic acid, the adsorption of glycerol monostearate by nano-TiO2 colloid is difficult, the reaction pathways for photocatalysis are complex and the band gap of TiO2 photocatalyst after adsorption is wide. The experimental and simulation results indicate that the different degradation levels are attributed to the difficulty of the adsorption and photocatalytic reactions of glycerol monostearate compared with the reactions of the other two easily degradable pollutants. Thus, the different photocatalytic degradation levels of organic pollutants in the two photocatalytic processes of papermaking wastewater indicate that sustainable photocatalytic technology could be applied to different types of industrial wastewater.