In-situ ESEM was firstly used to study super-thin Pd membranes undergoing gas/thermal treatment. Step by step analysis of evolution process and more details than ex-situ technologies. Elimination of Pd grains and diffusion along the whole surface under inert gas or H2 atmosphere. The formation of microhillocks occurred due to α–β phase transition or after exposure to O2 or H2O. Reconstruction of Pd membrane surface in H2 could remove microhillocks and pinhole formations.