The institution finished first in the annual rankings, ahead of Harvard, after finishing joint first with its Ivy League rival last year.
In the separate U.S. News ranking of national liberal arts colleges, Williams College finished first, as it did last year.
U.S. News says its rankings allow comparisons between institutions “based on such widely accepted indicators of excellence as freshman retention, graduation rates, and the strength of the faculty”.
Changes to the methodology in this year’s rankings include lowering the weighting for “student selectivity” from 15 per cent of a college’s total to 12.5 per cent, following criticisms from some quarters.
In the national universities ranking, Stanford University rose to fifth, up from joint sixth last year.
The Massachusetts Institute of Technology fell one place to joint seventh, from joint sixth last year.
Meanwhile, in the national liberal arts colleges ranking, Bowdoin College in Maine rose from joint sixth to joint fourth.
Davidson College in North Carolina rose from joint twelth to joint ninth.
Among historically black colleges and universities, Spelman College in Georgia was rated first.