In this paper, we study transition matrices of PBW bases of the nilpotent subalgebra of quantum superalgebras associated with all possible Dynkin diagrams of type A and B in the case of rank 2 and 3, and examine relationships with three-dimensional (3D) integrability. We obtain new solutions to the Zamolodchikov tetrahedron equation via type A and the 3D reflection equation via type B, where the latter equation was proposed by Isaev and Kulish as a 3D analog of the reflection equation of Cherednik. As a by-product of our approach, the Bazhanov–Sergeev solution to the Zamolodchikov tetrahedron equation is characterized as the transition matrix for a particular case of type A, which clarifies an algebraic origin of it. Our work is inspired by the recent developments connecting transition matrices for quantum non-super algebras with intertwiners of irreducible representations of quantum coordinate rings. We also discuss the crystal limit of transition matrices, which gives a super analog of transition maps of Lusztig’s parametrizations of the canonical basis.