The administration of Syrian Orthodox Church has been designed in a three-tied system in which the church, Diocese and the Parish Church from the three trusts. As a General Body of the Church, Malankara Syrian Christian Assocition is convened once in every 5 years. From every parish according to the Strength of its membership, laity and clergy participate in it as delegates. The association elect the Managing Committee, Metropolitan Trustee, Chruch Secretary and Church Trustee for the smooth administration of the day to day affairs of the Church. Moreover, there is a working committee consisting of members elected from the Managing Committee as well as  the officials elected by the Association which functions as the cabinet of the Church.

The Church is divided into various diocese under Metropolitans. The diocesan Association that meets once a year take important decisions regarding the administration of each diocese. The diocesan council elected by the General body of the diocese functions as the Governing body and give shape to the programmes of the diocese and implement those that are approved by the General Body. A priest who is elected as the diocesans Secretary maintains the minutes and presents the accounts and budget on behalf of the council. The tenure of office of the council and Secretary is three years.

Through the parish churches are governed by the diocese on spiritual matters, all other affairs are dealt by the parish themselves, as semi independent trusts. The administration of parish is vested with the general body of the parish. Normally the general body of the parish meets twice in a year. The Parish managing committee elected by the general body, implement the decisions of the general body. The parish trustee who is elected by the general body looks after the finance of the parish and execute the decisions as per the recommendation of the managing committee. The parish secretary who is elected along with the parish trustee, maintains and presents the minutes of the general body as well as that of the Managing Committee.