The wording of this passage differs slightly from other scriptures which speak of Jehovah as both the “Son” and the “Father.” Abinadi said that Jehovah was The Father, because he was conceived by the power of God: and the Son, because of the flesh; thus becoming the Father and the Son (Mosiah 15:3). The same concept is taught in the D&C, the Father and I are one—(I am) The Father because he gave me of his fullness, and the Son because I was in the world and made flesh my tabernacle, and dwelt among the sons of men (DC 93:3-4). Yet Jehovah tells Nephi that he was to come to do the will, both of the Father and of the Son—of the Father because of me, and of the Son because of my flesh.
In this verse, Jehovah is equating his will with the will of Elohim. He had in fact been the God of the Old Testament and the God of the Nephites, under the direction of his Father. But the fact that Jehovah equates his will with that of his Father has interesting implications. In particular, all the events of the Savior, in which he openly admits to following the will of the Father (as if it were different than His will), were in fact, situations in which He was following the will of Jehovah also, for the will of Jehovah and the will of Elohim are one (see Jn 4:34; 5:30; 6:38).
“This is a most difficult passage. It sounds as though the Lord is stating that he will come into the world to fulfill two wills- the will of Jehovah, the premortal God of the ancients (perhaps referred to here as ‘me’), and the will of the mortal Messiah (the person of ‘flesh’). Of course we know that they, Jehovah and Jesus, are one and the same being. At the same time, this statement dramatizes the separate and severable roles that would be played by the Master, that of the Holy One of Israel (premortal) and that of Jesus of Nazareth (mortal).” (McConkie, Millet, and Top, Doctrinal Commentary on the Book of Mormon, vol. 4, p. 7)