In recent years, attempts have been made to promote the performance of aerospace vehicles by modifying topology of various structural components. Honeycomb structure is one of the most usage structural components in the field of aerospace vehicles. The main aim of this research is to improve the amount of energy absorbed by traditional honeycomb structure under in-plane compression loading via modifying its topology. In this regard, a novel bio-inspired structure based on the combination of Fibonacci spiral pattern and regular honeycomb structure was presented. As the main novelty of this research, the nested hexagons were connected by Fibonacci spiral pattern, observed in biological organisms and natural structures. In the presence of Fibonacci spiral due to its nature, it can be expected that the honeycomb structure exhibit auxetic behavior under in-plane compression loading. Polylactic acid (PLA) as a biodegradable thermoplastic was used as the raw material to fabricate the specimens with one, two, or three nested hexagons using fused deposition 3D printing. The specimens printed in two arrangements were tested under in-plane compression loading conditions with loading rates of 5, 50, and 500 mm/min. Besides, a finite element analysis was performed to employ the results obtained from the empirical method for the industrial applications. The results manifested that in the presence of three nested hexagons linked by Fibonacci spiral pattern, the specific peak load and energy absorption of the honeycomb structure can be improved around 765 and 1219% compared to the regular honeycomb structure, respectively. At the end, the application of the novel topology in the case of an airfoil was investigated and it was observed that its performance has been improved significantly.