The chiral nature of active matter plays an important role in the dynamics of active matter interacting with chiral structures. Skyrmions are chiral objects, and their interactions with chiral nanostructures can lead to intriguing phenomena. Here, we explore the random-walk dynamics of a thermally activated chiral skyrmion interacting with a chiral flower-like obstacle in a ferromagnetic layer, which could create topology-dependent outcomes. It is a spontaneous mesoscopic order-from-disorder phenomenon driven by the thermal fluctuations and topological nature of skyrmions that exists only in ferromagnetic and ferrimagnetic systems. The interactions between the skyrmions and chiral flowers at finite temperatures can be utilized to control the skyrmion position and distribution without applying any external driving force or temperature gradient. The phenomenon that thermally activated skyrmions are dynamically coupled to chiral flowers may provide a new way to design topological sorting devices.