Affiliated college are affiliated to other university. They have to follow the syllabus of that affiliating university and all the norms. The admissions process is controlled by the University itself. The exams too are conducted by the university.

Autonomous colleges on the other hand have some or lot more freedom in various fields, like syllabus, evaluation process, admission.

An affiliated college which is accredited by National Assessment and Accreditation council of India (NAAC). This assessment is five yearly. The college can apply for autonomous status and U.G.C. may or may not grant it authority.

Autonomous colleges takes the decisions solely upon head of the college rather than asking the affliated heads whether the decision is right or wrong. Government college don't take admission through management .They have certain protocol like entrance exam  or merit  system for admission. Although for affiliated colleges it is easier to have better syllabus as they have to follow the syllabus from an already established university along with their modest fee structure.

Hope it helps.

Good luck for your future endeavour!