Scaffolds for bone tissue engineering should have sufficient mechanical properties comparable with those of the surrounding native bone tissue. Therefore, it is necessary to improve the mechanical properties, especially compressive strength, of 3D scaffolds for bone tissue engineering applications. Various studies have focused on the variation or manipulation of structures or materials, for example, the Kagome-structure scaffold or polycaprolactone/hydroxyapatite composite scaffold. In this study, we propose a modified honeycomb structure for 3D bone-tissue-engineering scaffolds. This is a 3D honeycomb structure with pores at its walls to enhance the interconnectivity. The honeycomb structure is known to be the strongest structure with respect to its weight. Therefore, the honeycomb structure inspired us to apply it to bone-tissue-engineering scaffolds, and its 3D interconnectivity was enhanced by adding pores in its walls without a considerable decrease in its mechanical strength. By means of numerical analysis, the compressive stiffness of the modified-honeycomb-structure scaffold was investigated, and it was found that the effective compressive modulus of the modified-honeycomb-structure scaffold was significantly superior to those of Kagome-structure and grid-structure scaffolds having similar porosity of 50% and main pore size of 500 µm. Meanwhile, the Kagome-structure scaffold had the highest compressive modulus among the reported 3D interconnected scaffolds. Moreover, the modified-honeycomb-structure scaffolds were successfully fabricated with polycaprolactone (PCL) using a lab-made bio-printer with a precision extrusion deposition (PED) system employing a nozzle with a size of 50 µm, and a compressive test using a UTM was performed to prove the numerical result, in which the effective compressive modulus of the modified-honeycomb-structure scaffold was found to be superior to that of the Kagome-structure scaffold. Furthermore, we assessed cell proliferation, and the modified-honeycomb-structured scaffold was more favorable for cell proliferation than the Kagome-structure and grid-structure scaffolds. • Modified-honeycomb scaffold was proposed and successfully fabricated with PCL. • Compressive stiffness of proposed scaffold was evaluated numerically. • Compressive stiffness of proposed scaffold was validated experimentally. • Proposed scaffold has the highest compressive stiffness among the control groups. • Proposed scaffold promote in-vitro cell behavior similar to the control groups.