Samuel did not yet know the LORD because he had never had a message from the LORD before.
So now the LORD called a third time, and once more Samuel jumped up and ran to Eli. "Here I am," he said. "What do you need?" Then Eli realized it was the LORD who was calling the boy.
So he said to Samuel, "Go and lie down again, and if someone calls again, say, 'Yes, LORD, your servant is listening.'" So Samuel went back to bed.