Photoswitchable cages that confine small guest molecules inside their cavities offer a way to control the binding/unbinding process through irradiation with light of different wavelengths. However, a detailed characterization of the structural and thermodynamic consequences of photoswitching is very challenging to obtain by experiment alone. Thus, all-atom molecular dynamics (MD) simulations were carried out to gain insight into the relationship between structure and binding affinity. Binding free energies of the B12F122- guest were obtained for all photochemically accessible forms of a photoswitchable dithienylethene (DTE) based coordination cage. The MD simulations show that successive photo-induced closure of the four individual DTE ligands that form the cage gradually decreases the binding affinity. Closure of the first ligand already significantly lowers the unbinding barrier and the binding free energy, and therefore favours guest unbinding both kinetically and thermodynamically. Analysis of the different enthalpy contributions to the free energy shows that binding is enthalpically unfavourable and thus an entropy-driven process, in agreement with experimental data. Dissecting the enthalpy into the contributions from electrostatic, van der Waals, and bonded interactions in the force field shows that the unfavourable binding enthalpy is due to the bonded interactions being more favourable in the dissociated state, suggesting the presence of structural strain in the bound complex. Thus, the simulations provide microscopic explanations for the experimental findings and open a possible route towards the targeted design of switchable nanocontainers with modified binding properties.