Layered magnetic topological materials are systems that exhibit both magnetic ordering and topological properties within their smallest two-dimensional units. The study of these systems may lead to the observation of new physical properties and phenomena, thereby garnering considerable interest among researchers. The effect of interlayer exchange coupling interactions on bilayer honeycomb Heisenberg ferromagnets with interlayer coupled topological phases has been investigated using linear spin wave theory. The impact of introducing two additional types of interlayer exchange coupling interactions and interlayer easy-axis anisotropy interactions on the topological phase transition are also explored in this work. By calculating the magnon dispersion relations at various interlayer exchange coupling interaction intensities, it was found that the band gaps of both high and low energy bands close and reopen at the Dirac points when the system reaches the critical values of the interlayer exchange coupling interactions. In magnon systems, such physical phenomena are typically associated with topological phase transitions. Upon calculating the Berry curvature and Chern numbers for the bands in the aforementioned process, it was discovered that the sign of the Berry curvature reverses and the Chern numbers change once the critical values of interlayer exchange coupling interaction strengths are reached, confirming that a topological phase transition has indeed occurred. Introducing two other types of interlayer exchange coupling interactions in this process can lead to the emergence of various novel topological phases within the system. The enhancement of interlayer easy-axis anisotropy interactions is likely to impede the occurrence of topological phase transitions in the system. We have found that a major distinction between bilayer honeycomb ferromagnets and their single-layer counterparts is that the sign of the magnon thermal Hall coefficient does not change during a topological phase transition; rather, abrupt shifts in the thermal Hall coefficient curve can be seen as indicators of topological phase transitions in bilayer honeycomb ferromagnets, which is also reflected in the changes in magnon Nernst coefficients. The research outcomes of this work can provide theoretical support for the development of novel spintronic devices with enhanced information transmission capabilities using bilayer honeycomb ferromagnetic materials, as well as serve as a theoretical reference for studies on other bilayer ferromagnetic systems.