Last year, Harvard had shared the number one position with Princeton University.
Princeton scored 99 points and fell to second position in the 2011 rankings of US' large, research-oriented institutions.
Harvard scores high on criteria like graduation rates, financial and faculty resources.
Yale University was ranked third, followed by Columbia University.
Stanford University is tied at the fifth place with the University of Pennsylvania.
Massachusetts Institute of Technology occupied the 7th spot while Cornell University came in 15th.
Williams College in Massachusetts emerged as the nation's top-ranked national liberal arts college—a category of schools that place a higher emphasis on undergraduate education.
The University of California—Berkeley, which is the 22nd ranked national university, is the top-ranked public school.
This marks the 27th year that the American news magazine has published college rankings.
It takes into account factors such as SAT scores, selectivity, graduation and retention rates, alumni giving and peer reputation while grading America's colleges and universities.