We discuss the role played by the Rota-Baxter operator in the Hopf algebra approach of Connes and Kreimer to the renormalization of perturbative quantum field theory. In their work, Feynman graphs are organized into a Hopf algebra and a regularized Feynman rule is given by an algebra homomorphism from this Hopf algebra to a Rota-Baxter algebra. Built on classical results in Rota-Baxter algebras such as Altkinson’s factorizations and Spitzer’s identity, we explain how pQFT results such as the algebraic Birkhoff decomposition for renormalization and the Bogoliubov formula can be derived from theorems on RotaBaxter algebras. We further show that the Feynman rules have a matrix representation that converts the process of renormalization to matrix calculations. Related rooted trees and decompositions will also be discussed.