To get the Chu Jelly's off the Deku tree you will need to walk up to the base if the tree and roll bash into the tree. This means go up close and perform a roll. Your head will bash off the tree and all of the Chu Jelly's will fall off the tree.
Once all of the jellies have fallen off the tree, you can attack them with your sword. If they jump back onto the tree, repeat the same process to make them fall off again.
Once you have destroyed all of the Chu Jelly's a cutscene will trigger and you can proceed with the game's story.