The crystallographic pore sizes of zeolites are substantially smaller than those inferred from catalytic transformation and molecular sieving capabilities, which reflects flexible variation in zeolite opening pores. Using in situ electron microscopy, we imaged the straight channels of ZSM-5 zeolite with benzene as a probe molecule and observed subcell flexibility of the framework. The opening pores stretched along the longest direction of confined benzene molecules with a maximum aspect change of 15%, and the <i>Pnma</i> space group symmetry of the MFI framework caused adjacent channels to deform. This compensation maintained the stability and rigidity of the overall unit cell within 0.5% deformation. The subcell flexibility originates mainly from the topologically soft silicon-oxygen-silicon hinges between rigid tetrahedral SiO<sub>4</sub> units, with inner angles varying from 135° to 153°, as confirmed by ab initio molecular dynamics simulations.