Conformational and thermal behavior of self-assembled structures of three phosphonic acids, OPA (octadecylphosphonic acid), TPA (tetradecylphosphonic acid), and OcPA (octylphosphonic acid), with different alkyl chain lengths are investigated and compared. The orientation of self-assembled bilayers depends on whether the substrate is nonpolar (graphite) or polar (mica). For nonpolar substrates, bilayers lay parallel to the surface, and for polar substrates, bilayers lay perpendicular to the surface. Thermal behaviors of these structures on mica and graphite are also investigated, showing that, depending on the temperature they are submitted to, molecules stack, unstack, or agglomerate on mica and form larger domains on graphite.