The Apostle to the Hebrews explains this account of Esau, who is said to be a fornicator, and a profane person Hebrews 12:16 left to a dissolute mind, being rejected, or as this scripture speaks, hated of God. And so all his race. For, when it is said, as in this scripture, that his mountains and heritages were laid waste, it is meant spiritually so. As the mountain of the Lord's house is put for the Church, Micah 4:1-2 so here is meant by the mountain of Esau, the state of reprobation. Esau, and the seed of Esau, void of grace here, and no part in the glory of Christ hereafter. Mount Seir was a type of desolation inhabited, by Esau and his seed. Genesis 36:8.
Related Commentaries of Malachi 1:3
Malachi 1:3-5
3 And I hated Esau, and laid his mountains and his heritage waste for the dragons of the wilderness.
4 Whereas Edom saith, We are impoverished, but we will return and build the desolate places; thus saith the LORD of hosts, They shall build, but I will throw down; and they shall call them, The border of wickedness, and, The people against whom the LORD hath indignation for ever.
5 And your eyes shall see, and ye shall say, The LORD will be magnified from the border of Israel.