'micromolecule' originates from the combining form 'micro-' from Greek 'mikros' meaning 'small' together with 'molecule' from Latin 'molecula' (a diminutive of 'moles', 'mass').

'micromolecule' was formed in modern scientific English by attaching the Greek-derived prefix 'micro-' to the existing word 'molecule' (from Latin via French). 'Molecule' itself comes from Latin 'molecula', a diminutive of 'moles', and entered English through scientific usage.

Initially the elements of the word meant 'small' + 'little mass'; over time the combined term has taken the technical meaning 'a relatively small molecule, especially in contrast to macromolecules'.