Polyoxymethylene dimethyl ether (PODEn) is a promising diesel additive, especially in particulate matter reduction. However, how PODEn addition affects the filtration efficiency and regeneration process of a catalytic diesel particulate filter is still unknown. Therefore, this experimental work investigated the size-dependent particulate number removal efficiency under various engine loads and exhaust gas recirculation ratios when fueling with diesel and diesel/PODEn mixture. In addition, the regeneration behavior of the cDPF was studied by determining the break-even temperatures for both tested fuels. The results showed that the cDPF had lower removal efficiencies in nucleation mode particles but higher filtration efficiencies in accumulation mode particles. In addition, the overall filtration efficiency for P10 particles was higher than that for D100 particles. Positioning the upstream cDPF, increasing the EGR ratio slightly decreased the number concentration of nucleation mode particles but greatly increased that of accumulation mode particles. However, increasing the EGR ratio decreased the removal efficiency of nanoparticles, and this effect was more apparent for the P10 case. Under the same period of soot loading, the pressure drop of P10 fuel was significantly lower than that of diesel fuel. In addition, a significantly lower BET was observed for the P10 fuel, in comparison with D100 fuel. In conclusion, adopting cDPF is beneficial for fueling with P10 in terms of the overall filtration efficiency in the particulate number and the lower input energy requirement for active regeneration. However, with the addition of EGR, the lower filtration efficiencies of nanoparticles should be concerned, especially fueling with diesel/PODEn mixture.