does cry has two syllables?
No.
then does story has two syllables
Yes. STO RY has two syllables.
You can tell by its entry in a dictionary -- in print or online.
For example: sto·ry (2 syllables)
http://www.answers.com/story
Other examples:
http://www.answers.com/incredible
in·cred·i·ble (4 syllables)
http://www.answers.com/because
be·cause (2 syllables)
http://www.answers.com/interest
in·ter·est (3 syllables)
But if you look up "cry" there will be no dots separating the syllables -- because there is only one syllable.