The manufacture of water-containing butanol diesel blends requires no excess dehydration and surfactant addition. Therefore, compared with the manufacture of conventional bio-alcohols, the energy consumption for the manufacture of water-containing butanol diesel blends is reduced, and the costs are lowered. In this study, we verified that using water-containing butanol diesel blends not only solves the trade-off problem between nitrogen oxides (NOx) and particulate matter (PM) emissions from diesel engines, but it also reduces the emissions of persistent organic pollutants (POPs), including polycyclic aromatic hydrocarbons (PAHs), polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), polychlorinated biphenyls (PCBs), polychlorinated diphenyl ethers (PCDEs), polybrominated dibenzo-p-dioxins and dibenzofurans (PBDD/Fs), polybrominated biphenyls (PBBs) and polybrominated diphenyl ethers (PBDEs). After using blends of B2 with 10% and 20% water-containing butanol, the POP emission factors were decreased by amounts in the range of 22.6%-42.3% and 38.0%-65.5% on a mass basis, as well as 18.7%-78.1% and 51.0%-84.9% on a toxicity basis. The addition of water-containing butanol introduced a lower content of aromatic compounds and most importantly, leaded to more complete combustion, thus resulting in a great reduction in the POP emissions. Not only the self-provided oxygen of butanol promoted complete oxidation, but also the water content in butanol diesel blends could cause a micro-explosion mechanism, which provided a better turbulence and well mixed environment for complete combustion.