How did God hear Samuel?

Answer 1

They both simply spoke with each other: verse 10 ("..the LORD came and stood nearby.") indicates this was a pre-incarnate appearance of Jesus Christ:-

1Sa 3:1-10 NET The Call of Samuel

Now the boy Samuel continued serving the LORD under Eli's supervision. Word from the LORD was rare in those days; revelatory visions were infrequent. (v.2) Eli's eyes had begun to fail, so that he was unable to see well. At that time he was lying down in his place, (v.3) and the lamp of God had not yet been extinguished. Samuel was lying down in the temple of the LORD as well; the ark of God was also there. (v.4) The LORD called to Samuel, and he replied, "Here I am!" (v.5) Then he ran to Eli and said, "Here I am, for you called me." But Eli said, "I didn't call you. Go back and lie down." So he went back and lay down. (v.6) The LORD again called, "Samuel!" So Samuel got up and went to Eli and said, "Here I am, for you called me." But Eli said, "I didn't call you, my son. Go back and lie down." (v.7) Now Samuel did not yet know the LORD; the word of the LORD had not yet been revealed to him. (v.8) Then the LORD called Samuel a third time. So he got up and went to Eli and said, "Here I am, for you called me!" Eli then realized that it was the LORD who was calling the boy. (v.9) So Eli said to Samuel, "Go back and lie down. When he calls you, say, "Speak, LORD, for your servant is listening." So Samuel went back and lay down in his place. (v.10) Then the LORD came and stood nearby, calling as he had previously done, "Samuel! Samuel!" Samuel replied, "Speak, for your servant is listening!"