Using in situ electron microscopy, it was directly observed that subcell flexibility of the zeolite framework occurred when benzene as a guest molecule was adsorbed into the straight channels of ZSM-5 zeolite nanosheets, where the opening pores stretched along the longest direction of confined benzene molecules with a maximum aspect change of 15%. This flexibility originates mainly from the topologically soft silicon-oxygen-silicon hinges between rigid tetrahedral SiO4 units, which is very important for understanding molecular adsorption and shape selective catalysis.