A direct conformational analysis using scanning tunneling microscopy (STM) has been performed for individual adsorbed alpha-octithiophene molecules on Cu(100). s-cis and s-trans conformational isomers are induced by the rotational flexibility of individual thiophene rings. By adding bulky N-silyl substituents to octithiophene, we successfully identify the s-cis and s-trans conformational isomers using STM. The obtained relative abundances of the s-cis and s-trans conformations are analyzed using ab initio molecular orbital calculations.