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The investigation aims to formulate ground-structure based topology optimization approach by using a higher-order beam theory suitable for thin-walled box beam structures. While earlier studies use the Timoshenko or Euler beams to form a ground-structure, they are not suitable for a structure consisting of thin-walled closed beams. The higher-order beam theory takes into an additional account sectional deformations of a thin-walled box beam such as warping and distortion. Therefore, a method to connect ground beams at a joint and a technique to represent different joint connectivity states should be investigated for streamlined topology optimization. Several numerical case studies involving different loading and boundary conditions are considered to show the effectiveness of employing a higher-order beam theory for the groundstructure based topology optimization of thin-walled box beam structures. Through the numerical results, this work shows significant difference between optimized beam layouts based on the Timoshenko beam theory and those based on a more accurate higher-order beam theory for a structure consisting of thin-walled box beams.