In the present paper, we characterize Fano Bott manifolds up to diffeomorphism in terms of three operations on matrix. More precisely, we prove that given two Fano Bott manifolds $X$ and $X'$, the following conditions are equivalent: (1) the upper triangular matrix associated to $X$ can be transformed into that of $X'$ by those three operations; (2) $X$ and $X'$ are diffeomorphic; (3) the integral cohomology rings of $X$ and $X'$ are isomorphic as graded rings. As a consequence, we affirmatively answer the cohomological rigidity problem for Fano Bott manifolds.