The quasi-degeneracy between the single-particle states (n, l, j = l + 1/2) and (n − 1, l + 2, j = l + 3/2) indicates a special and hidden symmetry in atomic nuclei-the so-called pseudospin symmetry (PSS)-which is an important concept in both spherical and deformed nuclei. A number of phenomena in nuclear structure have been successfully interpreted directly or implicitly by this symmetry, including nuclear superdeformed configurations, identical bands, quantized alignment, pseudospin partner bands, and so on. Since the PSS was recognized as a relativistic symmetry in 1990s, there have been comprehensive efforts to understand its properties in various systems and potentials. In this Review, we mainly focus on the latest progress on the supersymmetric (SUSY) representation of PSS, and one of the key targets is to understand its symmetry-breaking mechanism in realistic nuclei in a quantitative and perturbative way. The SUSY quantum mechanics and its applications to the SU(2) and U(3) symmetries of the Dirac Hamiltonian are discussed in detail. It is shown that the origin of PSS and its symmetry-breaking mechanism, which are deeply hidden in the origin Hamiltonian, can be traced by its SUSY partner Hamiltonian. Essential open questions, such as the SUSY representation of PSS in the deformed system, are pointed out.