The influences of impurities and oxidation evolution of waste cooking oil on the preparation of bio-jet fuel via hydroconversion were studied. The hydrogenation active sites and acid sites were covered by heavy metals, sulfides, and basic nitrogen compounds, resulting in the increase of selectivity for bio-jet fuel by decreasing the selectivity of diesel, aromatics, and iso-alkanes. The effects of impurities, oxidation on the reaction pathway, and product distribution became more distinct with higher catalyst acidity. The evolution and variation of naphthalene, indan, and phenanthrene obtained from cyclic fatty acids influenced the properties of fuel or evoked the catalyst deactivation. This work will help to design new catalysts for selective conversion of waste cooking oil into bio-jet fuel.