What does 1 Samuel 3:7 mean?

Before the Lord calls to Samuel a third time (1 Samuel 3:4–6, 8), Scripture explains why it did not immediately occur to Samuel that it was God's voice he heard. The boy did not yet "know the Lord." That is given further context by noting that Samuel had never before heard a direct revelation from God. Samuel would hear often from the Lord over the course of his life, but this would be his first experience of direct revelation from God that was meant to be passed on to someone else. That was the work of a prophet.

Eli's sons Hophni and Phinehas were also said not to have known the Lord (1 Samuel 2:12). In their case, they "were worthless men." Both they and Samuel knew much about the Lord, of course. Samuel had been serving the Lord for years by this time, and Eli's sons knew enough about the Lord to serve the people on His behalf, as well. The difference was that Eli's sons didn't know the Lord in the sense that they did not seem to believe in Him or fear Him. They profaned His sacrifices and sinned against the people in their work as priests (1 Samuel 2:12–17, 22). They also certainly don't seem to have ever heard from Yahweh directly.

Samuel's relationship to the Lord God of Israel would soon be very personal in a way that Eli's sons' never was. The contrast between Samuel's obedience to the Lord and Eli's sons' disregard for the Lord is striking. Whereas negative reports of all that Eli's sons did against Israel spread far and wide (1 Samuel 2:22–23), all of Israel recognized that Samuel was a prophet of the Lord (1 Samuel 3:20). God judged Eli and his sons for their contempt (1 Samuel 2:25–36), but He was with Samuel and revealed Himself to him (1 Samuel 3:19, 21).