Aiming at reducing damage between ship berthing and high-pressure vessels, the protective honeycomb filled with Roller Arrowhead Wings Honeycomb (RAWH) was constructed based on equivalent method. A novel Double Arrowhead Wings Honeycomb (DAWH), inspired by Tilia Platyphylloswas, was proposed for arrangement in RAWH. The analytical models were derived with size factor n for honeycomb selection and design. The mechanical properties, energy absorption, compression response, structure efficiency, and deformation mode of RAWH were investigated by Finite Element Analysis (FEA) and Experiment (EXP), comparing with Roller Hexagonal Honeycomb (RHH), Roller Re-entrant Honeycomb (RRH), and Roller Solid. With particular calculation methods, the work energy absorption, engineering strain, and engineering stress were obtained within acceptable error compared to finite element analysis. The contact force of RAWH exceeded RHH, RRH and Solid about 1.7, 5, and 0.32 times, with a maximum of 15000 N. Further, the deformation modes of RAWH were discussed and recorded with “V” mode and “U” mode appearing special characteristics of enhancement and resilience. The equivalent Poisson’s ratios for protective honeycombs were studied and described in the Morgan-Mercer-Flodin (MMF) growth model with the phenomena of “Step Fluctuation”, “Inter-layer Progression” and “Step Stability”. These results, methods, and discussions might bring significance for reducing damage from collisions in ocean engineering.