Supersymmetry (SUSY) of a Hamiltonian dictates double degeneracy between a pair of superpartners (SPs) transformed by supercharge, except at zero energy where modes remain unpaired in many cases. Here we explore a SUSY of complete isospectrum between SPs-with paired zero modes-realized by 2D electrons in zero-flux periodic gauge fields, which can describe twisted or periodically strained 2D materials. We find their low-energy sector containing zero (or threshold) modes must be topologically non-trivial, by proving that Chern numbers of the two SPs have a finite difference dictated by the number of zero modes and energy dispersion in their vicinity. In 30° twisted bilayer (double bilayer) transition metal dichalcogenides subject to periodic strain, we find one SP is topologically trivial in its lowest miniband, while the twin SP of identical dispersion has a Chern number of 1 (2), in stark contrast to time-reversal partners that have to be simultaneously trivial or nontrivial. For systems whose physical Hamiltonian corresponds to the square root of a SUSY Hamiltonian, such as twisted or strained bilayer graphene, we reveal that topological properties of the two SUSY SPs are transferred respectively to the conduction and valence bands, including the contrasted topology in the low-energy sector and identical topology in the high-energy sector. This offers a unified perspective for understanding topological properties in many flat-band systems described by such square-root models. Both types of SUSY systems provide unique opportunities for exploring correlated and topological phases of matter.