There is a great need to design methane combustion catalysts with good performance for reducing methane greenhouse gas emissions. However, the low temperature activity of the commonly used Pd catalysts is low in methane combustion reaction (<400 °C). In this work, we report the silicon modified MgAl₂O₄ was used as support of PdO, which resulted in well-dispersed and ultrasmall-sized PdO nanoparticles (∼2 nm). Catalytic tests results showed that PdO/Si–MgAl₂O₄ exhibited relatively high catalytic activity (T₉₀ = 318 °C) compared with unmodified MgAl₂O₄ supported PdO catalyst (T₉₀ = 368 °C) at GHSV of 30,000 mL/(g–h). Moreover, the PdO/Si–MgAl₂O₄ showed excellent cyclic catalytic stability during heating−cooling processes and robust long-term catalytic stability at high temperature of 740 °C. With comprehensive characterizations by using BET, XRD, SEM, HAADF-STEM, EDS mapping, XPS, Raman and NMR, we found that silicon as a structure promoter decreased the size of PdO nanoparticles by forming Si–O–Al bond without changing the electronic properties of PdO. These above results provide a guidance to develop better catalysts for methane combustion in the future.