Seeking economical, efficient and stable catalysts to ameliorate the slow kinetics of oxygen reduction in cathode of proton exchange membrane fuel cells is still a great challenge. Herein, we design and synthesize an advanced Pd-based catalyst, where small palladium-phosphorus nanoparticles (Pd3P NPs) with similar to 5.2 wt% Pd loading are embedded in three-dimensional (3D) bubble-like nitrogen, phosphorus co-doped carbon (NPC) film (Pd3P@NPC). The resultant catalyst delivers markedly enhancive catalytic performance in comparison with commercial Pt/C, Pd/C, Pd3P and NPC toward ORR, benefiting from the specific 3D porous structure, nano-size effect and the electronic interaction between Pd3P NPs and NPC. Specifically, the half-wave potential of Pd3P@NPC (0.885 V) is 36 mV higher than that of commercial Pt/C, and the mass activity of Pd3P@NPC is 1.112 mA mu g(Pd)(-1) at 0.85 V, which is 8.18-fold and 11.96-fold enhancement in regard to that of commercial Pt/C and Pd/C, respectively. It is interesting to note that the as-prepared Pd3P@NPC also maintains a predominant stability after 40,000 potential sweeping cycles. This new catalyst is expected to enlarge the species of 3D Pd-based composites such as palladium carbide, palladium nitride and palladium sulfide on heteroatoms doped carbon substrate for ORR.