c. 1400, from Old English inra, comparative of inne (adv.) "inside" (see in (adv.)). Similar formation in Old High German innaro, German inner. The original order of comparison was in/inner/inmost; the evolution has been unusual for a comparative, and inner has not been used with than since Middle English.
Inner man "the soul" is from late Old English; as "the spiritual part of man" by late 14c. The Quaker inner light is attested by that name from 1833. Inner tube in the pneumatic tire sense is from 1894. Inner city is attested from 1690s; as a euphemism for "urban poverty and crime," from 1963.