In 2024, Garvan, Sellers and Smoot discovered a remarkable symmetry in the families of congruences for generalized Frobenius partitions $c\psi_{2,0}$ and $c\psi_{2,1}$. They also emphasized that the considerations for the general case of $c\psi_{k,\beta}$ are important for future work. In this paper, for each $k$ we construct a vector-valued modular form for the generating functions of $c\psi_{k,\beta}$, and determine an equivalence relation among all $\beta$. Within each equivalence class, we can identify modular transformations relating the congruences of one $c\psi_{k,\beta}$ to that of another $c\psi_{k,\beta'}$. Furthermore, correspondences between different equivalence classes can also be obtained through linear combinations of modular transformations. As an example, with the aid of these correspondences, we prove a family of congruences of $c\phi_{3}$, the Andrews' $3$-colored Frobenius partition.