Structure-controlled synthesis of Pd nanocrystals has received much attention recently due to their remarkable catalytic performance. To get deep insight into the mechanism of kinetically controlled overgrowth and the relationship between structure and electrocatalytic performance, palladium concave nanocubes (PdCNs) with high-index facets were synthesized through a facile none-seeded routine induced by hexadecylpyridinium bromide (CTAB). The structural changes of PdCNs along with the concentration of CTAB, reaction time and temperature were investigated by transmission electron microscopy and X-ray diffraction. It was indicated that Pd nanocubes first grew into larger size with numerous interstices inside the PdCNs, and then the inner interstices were filled along with oxidative etching on the surface. The electrocatalytic activities of PdCNs with different structures were evaluated toward the electro-oxidation of methanol. The result showed that the electrocatalytic activity weakened with the decrease in interstices, which demonstrated that interstices played a more crucial role than the concave structures.