Inelastic incoherent neutron time-of-flight scattering was employed to investigate the low-frequency vibrational density of states (VDOSs) for a series of glassy Janus-poly(tricyclononenes), which consist of a rigid main chain and flexible alkyl side chains. Here, the length of the flexible side chains was systematically varied from propyl to octyl. Such materials have potential applications as active separation layers in gas separation membranes as a green future technology, especially for the separation of higher hydrocarbons. From the morphological point of view, the Janus polynorbornenes undergo a nanophase separation into alkyl side chain-rich nanodomains surrounded by a rigid polynorbornene matrix. Here, the influence of the nanophase-separated structure on the low-frequency VDOS is investigated from a fundamental point of view. The low-frequency VDOSs of these Janus polynorbornene show excess contributions to the Debye type VDOS known as the Boson peak (BP) for all side chain lengths. Due to the high incoherent scattering cross-section of hydrogen, most of the scattering comes from the alkyl side chain-rich domains. Compared to conventional glass-forming materials, in the considered Janus polynorbornenes, the BP has a much lower intensity and its frequency position is shifted to higher values. These experimental results are discussed in terms of the nanophase-separated structure where the alkyl chain-rich domains were constrained by the surrounding matrix dominated by the rigid backbone. With increasing alkyl chain length, the size of the alkyl chain-rich domains increases. The frequency position of the BP shifts linearly to lower frequencies with the size of these nanodomains estimated from X-ray measurements. The obtained results support the sound wave interpretation to the BP.