The college was first affiliated to Calcutta University, Kolkata. It was under this university itself that the institution developed into a full-fledged Degree College and barring Persian, secured affiliation for the Honours course too in all the subjects taught then. However, with the establishment of Gauhati University in 1948, it became one of its original constituent colleges. Although Post-Graduate classes in certain subjects like English, Economics and Botany were introduced in the college at different points of time under Calcutta University itself, such classes had to be finally discontinued as part of economy drive and also because of the establishment of Gauhati University. It was only in 1969 that the Assam State Government decided to introduce PG classes in Physics in the college on a permanent affiliation basis. Subsequently, the benefit of PG classes was extended to other subjects as well and finally on 17th October, 1992 , the then Hon'ble President of India, Late Dr. Shankar Dayal Sharma at a glittering function held in the premises of the college formally declared Cotton College as a Post-Graduate institution. Today, PG teaching is done in the college in as many as 21 departments. Now, the college, which began with 39 students and 5 teachers only, currently has a student enrolment of more than 5000 right from Higher Secondary to the PG classes and a faculty strength of 235.
The present day college has an infrastructure built on a sprawling campus covering an area of about 34 acres. The facilities include a modern Library well stocked with books, journals and rare manuscripts; well equipped Laboratories in different Academic Departments; a full fledged Department of Computer Science & IT; a vibrant Placement Cell, an Entrepreneurship Development Cell (EDC) and a Bioinformatics Infrastructure Facility (BIF) Center. In addition to these facilities, there are also a four bedded hospital, a Guest House, separate hostels for girls and boys, quarters for faculty, an Indoor Stadium, a canteen, a coffee house and an ultramodern State Bank of India ATM. All the Academic Departments, Centers and the College office are connected with round the clock Internet connectivity. In the year 2003, an 'Internal Quality Assurance Cell' has also been established to look after the internal quality of the institution.
A Board of Governors constituted by the Govt. of Assam sits from time to time to decide on the policy matters relating to the academic and administrative activities of the college.