Thermal oxidative stability is a key issue for jet fuel serving as a coolant of high-performance aircraft. This study investigated the effects of the hydrogenation degree on the oxidation and deposition of jet fuel (RP-3). Fuels with different hydrogenation degrees were achieved by a commercial catalyst, with the aromatic content reduced from 12.6 wt% to 0.4 wt%, resulting in a slight density decrease and a slight increase of the net heating value. Meanwhile, the total sulfur content of hydrogenated fuel was lowered to below 1 ppm, and the naturally occurring phenols were completely removed. The initial oxidation reactivity and deposition tendency of hydrogenated fuels were investigated by pressure differential scanning calorimetry and jet fuel thermal oxidation tester, respectively. For the initial oxidation, both the oxidation OT (onset temperature) and IP (induction period) of jet fuel decrease with increasing hydrogenation degree and show good linear correlations with the aromatic content. For thermal deposition, pristine RP-3 cannot pass the JFTOT test (355 °C for 5 h), while all hydrogenated RP-3-t can pass 355 °C JFTOT test, owing to the almost total removal of inherent heteroatomic species (sulfurs and phenols) by hydrogenation. This work confirms that deep hydrogenation is a promising approach to improve the thermal oxidative stability of jet fuel (fewer deposits) for the practical applications.