Moses heard God’s voice from above the mercy seat because that was the place where the Lord chose to manifest His presence and speak to His people. The mercy seat, which covered the ark of the covenant, was the throne of God’s presence on earth, located between the cherubim. From there, God gave His commands and guidance to Moses for Israel.
“Now when Moses went into the tabernacle of meeting to speak with Him, he heard the voice of One speaking to him from above the mercy seat that was on the ark of the Testimony, from between the two cherubim; thus He spoke to him.” (Numbers 7:89)
This revealed that God’s guidance was inseparable from His holiness and mercy. The ark contained the testimony of His covenant, and the mercy seat represented atonement. By speaking from there, the Lord showed that His rule over Israel was both righteous and merciful, and that all direction for His people flowed from His covenant presence.
