It is administered by the Malankara Metropolitan and Catholicos-Elect, Gregorios Joseph, under the spiritual authority of the Patriarch of Antioch, Ignatius Aphrem II the supreme hierarch of the Syriac Orthodox Church.

[19] The dominant view[8] is that the entirety of the Saint Thomas Christian community gradually gravitated towards the Persian Church of the East headed by the Catholicos-Patriarch of Seleucia-Ctesiphon, and became part of its archdiocese of Rev Ardashir, by 420 CE,[24][25][26] which lasted till the arrival of Portuguese colonists in the 16th century.

[8] The Jacobite church further argues that the Persian bishops who governed Saint Thomas Christians, recognized the supremacy of the Patriarch of Antioch before 500 CE.

In the 16th century, the Portuguese Jesuits deliberately attempted to annex the native Christians to the Catholic Church, and in 1599 they succeeded through the Synod of Diamper.

Meanwhile, the Dutch East India Company defeated the Portuguese and gained supremacy over the spice trade in Malabar in 1663.

In 1910, Reverend Konattu Mathen Malpan translated the prayer book of the Syrian orthodox church into Malayalam, known as Pampakuda Namaskaram, with permission from Ignatius Abded Aloho II.

The church confesses Trinitarianism, that God, who is one in essence, subsists in three hypostasis, the Father, Son, and Holy Spirit.

[37] The church believes in the incarnation of God the Son, who is Jesus Christ, of the Virgin Mary, who they teach was cleansed by the Holy Spirit of all natural impurity, filling her with the Father's grace.

The highest rank in the ecclesiastical hierarchy is the patriarch of Antioch, head of the Syriac Orthodox Church, who became the first among equals of the Diocese of the East as stated by the Council of Nicaea (Canon 6).

The church holds the place of the Virgin Mary as the Mother of God as affirmed by the Council of Ephesus, with the title of Theotokos(Θεοτόκος) in Greek, Yoldath Aloho(ܝܠܕܬ ܐܠܗܐ) in Syriac, or Daiva Mathavu (ദൈവമാതാവ്) in Malayalam.

The conflict with MOSC started in 1912, when the Malankara Metropolitan Dionysius Vattesseril was suspended by the Patriarch of Antioch, Ignatius Abded Aloho II.

This caused Vattesseril to go to the deposed Patriarch, Ignatius Abded Mshiho II, to get an autocephalous Catholicate established in Malankara.

After years of conflict the church reunited in 1955, under the Patriarchate of Antioch, with an autonomous Maphrianate, leading to the subsequent enthronement of Baselios Augen I as Catholicos of the East.

There are also set rules and guidelines, within this agreement specifically for interfaith marriages between the Malankara Syriac Orthodox and the Syro-Malankara Catholic churches.

In the seventh century, the Syriac Orthodox Christians who lived outside the Roman Empire began using the title of "maphrian", for their head.

This office ranked right below the Patriarch of Antioch in Syriac Orthodox church hierarchy, until it was abolished in 1860 and reinstated in 1964 in India.