Metal-based fuel borne catalysts (FBC) have been extensively studied as an effective technology to reduce diesel particles and assist diesel particulate filter (DPF) regeneration. In this study, FBC fuels were prepared with Fe element mass fractions of 0, 100, 200, 300 and 400 mg/kg (marked as Diesel, Fe100, Fe200, Fe300 and Fe400). The effects of FBC additions on fuel economy and emission characteristics were carried out on a common-rail engine. Also, particle size distribution, microstructure, surface functional groups, element content and oxidation properties of exhaust particles were systematically analyzed. Results showed that the brake thermal efficiency was improved with the addition of FBC in diesel fuel, especially at low load, and the NOx and smoke emissions showed a decreasing trend. Compared with Diesel particles, the total mass concentration and the mean particle diameter of Fe300 particles decreased, the overall particle size distribution moved from coarse mode to accumulation mode, however, the total number concentration increased. Fe300 particles had larger layer spacing and microcrystalline curvature, smaller microcrystalline size and lower graphitization. In addition, the relative contents of OH and aliphatic C–H in Fe300 particles were higher than those in Diesel particles. The relative content of C atoms in Fe300 particles decreased, while the relative content of O atoms increased. Temperature-programmed-oxidation experiments indicated that semi-volatile organic components appeared in Fe300 particles, the peak temperature of weight loss rate decreased by 131 °C as compared with Diesel particles, the activation energy was also significantly lower, and therefore the particle oxidation activity was improved.