3D printing of continuous carbon fiber-reinforced composites relieves molds in composite manufacturing and gives flexibility to the design of lightweight and robust circular honeycomb structures. Nevertheless, how process defects affect the failure mechanisms of 3D-printed continuous carbon fiber-reinforced honeycomb structures remains undisclosed. To advance this research area, it requires a comprehensive investigation of the failure mechanisms and process defects of 3D-printed continuous carbon fiber-reinforced composite circular honeycomb structures (CCFRCCHSs), with particular attention to the influence of stacking orientations. In this study, 3D printing has been introduced to fabricate CCFRCCHSs using the identical composite material and geometry but different stacking orientations. Both in-plane and out-of-plane quasi-static compression experiments were carried out on these CCFRCCHSs. The mechanical properties and failure mechanisms were investigated through experimental analysis and cross-section observation, from which the microscopic voids and weak interfaces were identified as the dominating factors influencing the failure modes of CCFRCCHSs. This study provides insights into the association between process defects and failure mechanisms of 3D-printed CCFRCCHSs with different stacking directions, which offers guidance for the design of lightweight and robust composite circular honeycomb structures.