The preparation of honeycomb scaffold with hierarchical controllable porous structures is reported. The ABA three block amphiphilic copolymer PS-b-P(St-Alt-AMn)-b-PS was synthesized through reversible addition fragmentation chain transfer polymerization (RAFT) and subsequently self-assembled to core–corona nanoparticles with the middle block P(St-Alt-AMn) as the core and two side block PS as the corona. The formed core–corona nanoparticles were further crosslinked through the reaction of amino diphenyl methane with anhydride in chains. The core-crosslinked core–corona nanoparticles were used as the building block to fabricate the controllable porous scaffold with hierarchical structure. The micrometer level honeycomb mesostructures can be obtained by an inverse emulsion template method which is consisted in the formation of the high internal phase ratio emulsions (HIPRE) while the nanometer level pores are formed by the close-packed core–corona block copolymer nanoparticles. As carboxylic group is formed in the crosslink step of the core, the growth factor can be easily incorporated into the matrix in order for the growth of the cell in the tissue engineering application. This kind of hierarchical honeycomb structure is an ideal candidate for the tissue engineering and drug delivery applications.