Exploring the state-of-the-art combustion catalysts that efficiently stabilize precious metal has been a wide concern to limit rising levels in methane emissions. Herein we exhibit that utilizing ultrathin mesoporous spinel catalysts (Co2MO4, M = Co, Mn, and Al) as a support can stabilize PdO cluster by strengthening the metal − support interactions at being close to atomic scale. These are found that the as-synthesized Pd-embedded catalysts possesses highly active surface lattice oxygen, enhanced Co3+ in the surface layers, and shows outstanding low-temperature reducibility. More importantly, in-situ XRD results reveals that Pd-Co2MnO4 is more sensitive to thermal effects than that of Co2MnO4, which leads to the surface phase migration of PdO clusters and lattice oxygen release on Pd-Co2MnO4 catalyst. Among these catalysts, the Pd-Co2MnO4 catalyst performs the best catalytic activity for methane oxidation (T90 = 324 °C, Ea=37.4 kJ mol−1), especially with excellent cycle stability, and water-resistances. This study can be instructive for fabricating desirable heterogeneous catalysts and bring new insight into the design of highly efficient Pd-based catalysts.