The study utilizes the energy-flux-vector method to analyze the heat transfer characteristics of natural convection in a wavy-wall porous square cavity with a partially-heated bottom surface. The effects of the modified Darcy number, modified Rayleigh number, modified Prandtl number, and length of the partially-heated bottom surface on the energy-flux-vector distribution and mean Nusselt number are examined. The results show that when a low modified Darcy number with any value of modified Rayleigh number is given, the recirculation regions are not formed in the energy-flux-vector distribution within the porous cavity. Therefore, a low mean Nusselt number is presented. The recirculation regions do still not form, and thus the mean Nusselt number has a low value when a low modified Darcy number with a high modified Rayleigh number is given. However, when the values of the modified Darcy number and modified Rayleigh number are high, the energy flux vectors generate recirculation regions, and thus a high mean Nusselt number is obtained. In addition, in a convection-dominated region, the mean Nusselt number increases with an increasing modified Prandtl number. Furthermore, as the length of the partially-heated bottom surface lengthens, a higher mean Nusselt number is presented.