The ability of two complementary molecular modules bearing H-bonding uracilic and 2,6-(diacetylamino)pyridyl moieties to self-assemble and self-organize into submicrometer morphologies has been investigated by means of spectroscopic, thermogravimetric, and microscopic methods. Using uracilic N-BOC-protected modules, it has been possible to thermally trigger the self-assembly/self-organization process of the two molecular modules, inducing the formation of objects on a mica surface that exhibit crater-like morphology and a very homogeneous size distribution. Confirmation of the presence of the hydrogen-bonding-driven self-assembly/self-organization process in solution was obtained by variable-temperature (VT) steady-state UV-vis absorption and emission measurements. The variation of the geometric and spatial features of the morphologies was monitored at different T by means of atomic force microscopy (AFM) and was interpreted by a nonequilibrium diffusion model for two chemical species in solution. The formation of nanostructures turned out to be affected by the solid substrate (molecular interactions at a solid-liquid interface), by the matter-momentum transport in solution (solute diffusivity D and solvent kinematic viscosity ν), and the thermally dependent cleavage reaction of the BOC functions (T-dependent differential weight loss, θ = θ(?)) in a T interval extrapolated to ∼60 K. A scaling function, f = f (νD , ν/D , θ), relying on the onset condition of a concentration-driven thermosolutal instability has been established to simulate the T-dependent behavior of the structural dimension (i.e., height and radius) of the self-organized nanostructures as 〈h〉 ≈ f (T) and 〈r〉 ≈ 1/f (T).