The Christology of the Assyrian Church of the East is distinctive and has been a source of both theological identity and historical controversy. The church teaches that in Jesus Christ there exist two complete natures (qnome)—divine and human—united in one prosopon or person (parsopa). The divine nature is the eternal Word/Logos, pre-existing from all eternity; the human nature is a complete human being, with true human body, soul, and spirit, assumed by the Logos at the Incarnation. These two natures are perfectly united in Christ without mixture, confusion, or separation.

This formulation differs from Chalcedonian terminology, which speaks of 'two natures in one person.' The East Syrian use of qnome to denote the distinct natures was considered suspect after the church's rejection of the Council of Ephesus (431 AD), and the tradition of Theodore of Mopsuestia was later misrepresented as separatism. Modern ecumenical dialogue has clarified that the East Syrian and Chalcedonian formulations are seeking to express the same truth using different conceptual frameworks. The church rejects the title 'Theotokos' (God-bearer) for Mary, preferring 'Christotokos' (Christ-bearer) or 'Mother of Christ,' reflecting its Christological emphasis on the distinction and union of the natures.