An examination container includes a main body, a membrane assembly and a cover. The main body has an accommodating trough for holding sample. The membrane assembly covers an opening end of the accommodating trough. The membrane assembly includes a support body and a membrane. The support body has a first surface and a second surface, wherein the support body is flat and has a first through-hole penetrating through the first surface and the second surface. The membrane is arranged on the second surface side of the support body and has a second through-hole. The second through-hole is opposite to the first through-hole and allows a charged particle beam to pass the second through-hole. The cover is detachably connected to the main body to secure the membrane assembly. The membrane assembly is easy to replace and uses less consumables. An electron microscope using the abovementioned examination container is also disclosed.