The main aim of this study is to investigate the effect of printed hierarchical-sinusoidal corrugated core patterns and the load direction on the flexural properties of the cotton/epoxy composites sandwich panels. For the cores, six sinusoidal corrugated structures were considered. Besides, possible arrangements (transvers or longitudinal wave, arch downward or upward) of the sinusoidal corrugated cores with respect to the loading direction were considered. Totally, 72 cores were fabricated using a 3D printer and poly lactic acid material. It was observed that for the transverse arrangement, the flexural strength of sandwich panels is significantly improved by changing the pattern from the simple form to the hierarchical patterns. In contrast, for the longitudinal pattern, improvement in the flexural properties was not obtained by changing the core pattern. It was also manifested that corrugated core arrangement has remarkable effect on the mechanical properties of the sandwich panels. For the transverse pattern core panel, the maximum values of normalized face-sheet bending strength (FBS), core shear ultimate strength (CSUS) and energy absorption were obtained as 7.17 MPa/kg, 223.91 MPa/kg and 114.56 J/kg, respectively. Besides, for the longitudinal pattern core panel, the maximum values of FBS, CSUS and energy absorption were obtained as 7.86 MPa/kg, 245.78 MPa/kg and 330.75 J/kg, respectively. Comparing the obtained results with the available data in the literature manifested that the flexural properties of the corrugated core sandwich structures are significantly improved by changing its core system from the other materials to the printed material.