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Supercooled liquids undergo complicated structural relaxation processes, which have been a long-standing problem in both experimental and theoretical aspects of condensed matter physics. In particular, past experiments universally observed for many types of molecular liquids that relaxation dynamics separated into two distinct processes at low temperatures. One of the possible interpretations is that this separation originates from the two-scale hierarchical topography of the potential energy landscape; however, it has never been verified. Molecular dynamics simulations are a promising approach to tackle this issue, but we must overcome laborious difficulties. First, we must handle a model of molecular liquids that is computationally demanding compared to simple spherical models, which have been intensively studied but show only a slower process: $α$ relaxation. Second, we must reach a sufficiently low-temperature regime where the two processes become well separated. Here, we handle an asymmetric dimer system that exhibits a faster process: Johari-Goldstein $β$ relaxation. Then, we employ the parallel tempering method to access the low-temperature regime. These laborious efforts enable us to investigate the potential energy landscape in detail and unveil the first direct evidence of the topographic hierarchy that induces the $β$ relaxation. We also successfully characterize the microscopic motions of particles during each relaxation process. Finally, we study the predictive power of low-frequency modes for two relaxation processes. Our results establish for the first time a fundamental and comprehensive understanding of experimentally observed relaxation dynamics in supercooled liquids.