In this paper, we introduce the $U$-Bernoulli, $U$-Euler, and $U$-Genocchi polynomials, their numbers, and their relationship with the Riemann zeta function. We also derive the Apostol-type generalizations to obtain some of their algebraic and differential properties. We introduce generalized $U$-Bernoulli, $U$-Euler and $U$-Genocchi polynomial Pascal-type matrix. We deduce some product formulas related to this matrix. Furthermore, we establish some explicit expressions for the $U$-Bernoulli, $U$-Euler, and $U$-Genocchi polynomial matrices, which involves the generalized Pascal matrix.