The weak van der Waals interactions in the out-ofplane direction result in markedly low thermal conductivity in onedimensional (1D) and two-dimensional (2D) materials, which substantially restricts their applications. Developing three-dimensional (3D) columnar hybrid structures, featuring high thermal conductivity both within and beyond the plane, effectively addresses this challenge. This study investigated a 3D hybrid structure composed of graphene and boron nitride nanotubes (GR-BNNTs) using non-equilibrium molecular dynamics simulations. This approach allowed the examination of the formation mechanisms and key factors influencing thermal rectification (TR) in these materials. Our findings reveal a novel mechanism for independently regulating forward and backward heat fluxes in GR-BNNTs. By manipulating the thermal properties of the BNNTs and the graphene layer, the TR ratio can be controlled flexibly. Additionally, we identify specific strategies for independently adjusting the heat flux, such as altering the intercolumn distance of BNNTs, which impacts the backward flux merely, while applying strain to affect the forward flux merely. This research introduces a novel concept of independent regulation of forward and backward heat fluxes, providing significant insights into phonon thermal transport in 3D hybrid structures.