In recent years, it has been a hot research topic to study the interaction between atomic ensemble and cavities, and many researches have been done in this regard. In such a system, some atoms are trapped in the cavity, which can be used to study their dynamic characteristics, e.g., the evolution of photon numbers and photon transition. The Jaynes-Cummings model is an important model for studying the dynamic characteristics of the cavity-atom system, which is based on the interaction between a single two-level atom and the cavity field. Recently, coherent photon control in cavity under specific conditions has become an important part of quantum computing and communication. It is worth noting that the tunable photon transmission and all-optical switches based on the cavity have already aroused much interest and have been used in many areas. The quantum information and networks are mostly rooted in complex optical devices, which may show nonreciprocal or asymmetric photon transport. In this paper, we demonstrate that by using an optical closed-loop system the unconventional photon transport can be realized with two mutually perpendicular cavities coupled through external fiber and a two-level atom placed on the intersection. This three-mode system supports two orthogonal propagation directions, that is to say, and the interactions among probe fields are mutually perpendicular. Without ignoring the spontaneous decay of the natural atom, the complex and controllable quantum interference induced by the efficient hybrid interaction of the light, cavity modes, and the atom in such a closed-loop structure can result in a few interesting symmetric and asymmetric photon transport behaviors, i.e. coherent perfect synthesis and coherent perfect reflection. Aside from these compelling properties, the group velocity can also be modulated, i.e., fast and slow light effect. All of these processes can be dynamically controlled by using the probe field phase difference, the tunneling coupling between two cavities and the coupling between the cavity and the atom. Importantly, due to so many advantages, such a tunable scheme can be readily extended to some optical devices, e.g., the switch and the router that is challenging to conventional optical devices.