A characteristic polynomial is an important invariant in the field of hyperplane arrangement. For the Linial arrangement of any irreducible root system, Postnikov and Stanley conjectured that all roots of the characteristic polynomial have the same real part. In relation to this conjecture, Yoshinaga obtained an explicit relationship between the characteristic quasi-polynomial and the Ehrhart quasi-polynomial for the fundamental alcove. In this paper, we calculate Yoshinaga's explicit formula through the decomposition of the Ehrhart quasi-polynomial into several quasi-polynomials and a modified shift operator, and obtain new formulas for the characteristic quasi-polynomial of the Linial arrangement. In particular, when the parameter of the Linial arrangement is relatively prime to the period of the Ehrhart quasi-polynomial, we prove the Postnikov-Stanley Linial arrangement conjecture. This generalizes some of the results for the root systems of classical types that have been proved by Postnikov-Stanley and Athanasiadis. For other cases, we verify this conjecture for exceptional root systems using a computational approach.