The origin of the Holy Spirit Seminary College of Theology and Philosophy dates back to the early foundation of the Regional Seminary for South China (1931-1964). The purpose of the foundation was the formation of local clergy for the South China District who could then serve in their local dioceses after their priestly ordination. The South China District comprised the dioceses of Shaoguan, Wuzhou, Guangzhou, Jiangmen, Jiaying, Shantou, Dingzhou, Xiamen, Fuzhou, Jianning, Funing, Beihai, Qingxian and Hong Kong.

However, in 1964, when the above dioceses were not sending any of their seminarians for formation, the Congregation of Propaganda Fide closed the Regional Seminary and transferred the premises to the Hong Kong Diocese, which in the same year on the same premises set up its diocesan seminary, naming it “Holy Spirit Seminary,” thus implementing the directive of Vatican II that the formation of seminarians and priests should be localized.

In 1970, the Holy Spirit Seminary College of Theology and Philosophy was established through the collaboration of the Hong Kong Diocese, the Macau Diocese, the Society of Jesus (Jesuits) and the Salesians of Don Bosco. Then in 1985, the Order of the Franciscan Minors was invited to join them.

In order that the laity might have an opportunity to deepen and widen their knowledge of God, since they too can be effective instruments in building God's Kingdom, the Seminary College was opened to the laity in 1973.

The Theology and Philosophy Divisions of the College were affiliated to the Pontifical Urban University of Rome in 1974 and 1976 respectively; this makes it possible for students taking theology and philosophy to obtain the degrees of Bachelor of Sacred Theology and Bachelor of Philosophy.

A further step was taken, when in 1989, in order to fulfil the desires and needs of the laity for a degree course in theology, the College was expanded with the opening of the Higher Institute of Religious Sciences, endorsed by the Faculty of Theology of the Pontifical Urban University. Those who have completed the necessary requirements in this Institute obtain the degree of Bachelor of Religious Sciences.

In 1994, with the consent of the Pontifical Urban University, the Theology Division started a two-year programme leading to the degree of Licentiate in Sacred Theology (S.T.L.). This required upgrading the status of the Theology Division from that of affiliation to aggregation with respect to the Pontifical Urban University. On March 6th, 1997, the Holy See's Congregation for Catholic Education upgraded the Theology Division, aggregating it "ad experimentum" for five years to the Theology Faculty of the Pontifical Urban University.