Mesoporous nanocompartment films composed of silica particles and hallow silica capsules were prepared by the layer-by-layer (LbL) technique. The resulting mesoporous nanocompartment films possess special molecular encapsulation and release capabilities so that stimuli-free auto-modulated stepwise release of water or drug molecules was achieved through the mesopore channels of robust silica capsule containers embedded in the film. Stepwise release of water was reproducibly observed that originates in the non-equilibrated rates between evaporation of water from the mesopore channels to the exterior and the capillary penetration of water from container interior to the mesopore channels. It was generalized to evaporation of other substances, fragrances, limonene. Application was also tested in the controlled release of the sunscreen UV-absorber (UV-S1) for circumvention of its rapid dissolution in water and prolongation of its prophylactic effect toward harmful ultraviolet radiation. UV-S1 was successfully entrapped within the mesoporous nanocompartment films and was released in a prolonged stepwise mode. The nanocompartment films developed in this research are promising materials for drug delivery since they allow gradual release of therapeutic agents with likely related improvements in their efficacy.