Either, first, He was not acquainted with God in that extraordinary or prophetical way. Or rather, secondly, He did not yet understand, any more than before, that it was not Eli, but God, who spake to him. And this ignorance of Samuel's served God's design, that his simplicity might give Eli the better assurance of the truth of God's call and message to Samuel.
Related Commentaries of 1 Samuel 3:7
1 Samuel 3:7
7 Now Samuel did not yet know the LORD, neither was the word of the LORD yet revealed unto him.