Abstract Honeycomb composites show excellent properties with higher specific stiffness and strength compared with traditional composites. This work designed and manufactured a novel three‐dimensional honeycomb composite with an integrated honeycomb core structure through three‐dimensional woven fabricating technology. The influences of boundary effects, hole size and sample width of honeycomb core composites were respectively investigated through experimental and numerical methods. The results show that the rise of free wall number at the edges caused compressive properties to decrease in the weft direction but increase in warp and out of plane directions. The strength of multi free wall samples (2 main bodies) only reaching 93.6% of the few free wall samples (3 main bodies). The mechanisms of hole size affecting the compressive properties include many complicated factors such as structural scale‐law and curing defects. Finally, the decrease of compressive strength along the weft direction with the rise of width was also due to the earlier buckling failure of the honeycomb wall. The investigation of this work benefits to the design and application of the proposed honeycomb composites in many special fields. Highlights A new three‐dimensional honeycomb core structure was designed and manufactured. The compressive behaviors of honeycomb composites were studied in detail. The number of free walls has great impacts on honeycomb composites. The mechanism of hole size effects on honeycomb composites is complicated. Fiber defects and buckling affect properties along weft direction apparently.