All shops,except this fruit shop,are closed on Sunday.

All shops are closed on Sunday except this fruit shop.

are these sentences correct.

what is the differences between two?

add the preposition 'for' and the sentences will be correct, although I think the second one sounds a lot better. Therefore I'd say:

"All shops are closed on Sunday except for this fruit shop."

The reason why the second one is preferable is that the repetition of 'shop' is spaced out. Otherwise the first is correct too . . .
Hanuman, why are you re-posting? We have already discussed your sentences at some length, if you will Except.