Ultrafast spectroscopy reveals the effects of confinement on the excited-state photoisomerization dynamics for a series of alkyl-substituted trans-stilbenes encapsulated in the hydrophobic cavity of an aqueous supramolecular organic host-guest complex. Compared with the solvated compounds, encapsulated trans-stilbenes have broader excited-state absorption spectra, excited-state lifetimes that are 3-4 times longer, and photoisomerization quantum yields that are 1.7-6.5 times lower in the restricted environment. The organic capsule disrupts the equilibrium structure and restricts torsional rotation around the central C=C double bond in the excited state, which is an important motion for the relaxation of trans-stilbene from S-1 to S-0. The location and identity of alkyl substituents play a significant role in determining the excited-state dynamics and photoisomerization quantum yields by crowding inside the capsule. The results are discussed in terms of tuning the relative crowding inside the capsule. The results are discussed in terms of distortions of the ground- and excited-state potential energy surfaces, including the topology of the S-1-S-0 conical intersection.