In this paper, a two-dimensional (2D) hierarchical computational model was developed for analysis of heat transfer in unidirectional composites filled with doubly periodic natural fiber bundle. The reinforcement in the composite encloses large number of small lumens, which hints the composite consisting of matrix and natural fiber bundles involves structures at several level scales. In the model, the unit representative volume element (RVE) of composite with fibers arranged periodically was taken into consideration and equivalent models were converted from differently scaled RVEs by a two-step homogenized procedure. Subsequently, numerical simulation of heat–transfer process in each model was performed by finite element analysis and the overall transverse thermal conductivity of each model was obtained numerically. To verify the developed composite models, an optional interrelationship between the overall thermal conductivity of the equivalent natural fiber bundle and the solid region phase in it was obtained for the first-step homogenization and then was compared with analytical results or numerical results from other methods. Finally, a sensitivity analysis was conducted with the models to investigate how changes in the values of important variables such as thermal conductivity and volume fraction of constituent can affect the effective thermal properties of the composite.