A new approach is proposed for two-dimensional molecular separation based on the Brownian ratchet mechanism by use of a self-spreading lipid bilayer as both a molecular transport and separation medium. In addition to conventional diffusivity-dependence on the ratchet separation efficiency, the difference in the intermolecular interactions between the target molecules and the lipid bilayer is also incorporated as a new separation factor in the present self-spreading ratchet system. Spreading at the gap between two ratchet obstacles causes a local change in the lipid density at the gap. This effect produces an additional opportunity for a molecule to be deflected at the ratchet obstacle and thus causes an additional angle shift. This enables the separation of molecules with the same diffusivity but with different intermolecular interaction between the target molecule and surrounding lipid molecules. Here we demonstrate this aspect by using cholera toxin subunit B (CTB)-ganglioside GM1 (GM1) complexes with different configurations. The present results will unlock a new strategy for two-dimensional molecular manipulation with ultrasmall devices.