To explore new cavity functions, we herein employed cis‐trans stereoisomers with a N=N, C=C, or C=N unit as guest indicators for a polyaromatic capsule. Thanks to the rigid, spherical cavity with a diameter of ∼1 nm, azobenzene and stilbene derivatives are quantitatively encapsulated by the capsule with 100 % cis‐selectivity in water. The isomerization of the cis‐azo compound is suppressed against heat and light in the cavity, due to the confinement effect. Furthermore, C,N‐diphenyl imine derivatives are quantitatively encapsulated by the capsule in water and adopt an otherwise unstable cis‐form. The polyaromatic cavity suppresses the hydrolysis of the imines in water, even at elevated temperature, due to the shielding effect. Accordingly, the properties of the cis‐trans isomers could be largely altered through supramolecular manipulation. Thanks to a polyaromatic capsule, an azobenzene derivative is quantitatively encapsulated by the spherical cavity with 100 % cis‐selectivity. The cis‐to‐trans isomerization is suppressed against heat and light due to the confined cavity effect. C,N‐diphenyl imines are also encapsulated by the capsule and adopt an otherwise unstable cis‐form. The cavity suppresses their hydrolysis in water due to the shielding effect.