A LUT with Hierarchical Structure (HS-LUT) is proposed in this paper to realize the unique nonlinear component, Substitution Box (S-box), of the block ciphers. Different types of S-boxes are analyzed and four important features of them are summarized. Then, custom 4R/1W memory is proposed as the storage unit of the reconfigurable S-box, and an example set of block ciphers is put forward to describe how to achieve a satisfactory structure of reconfigurable S-box. The proposed HS-LUT is applicable for different sets of ciphers and it is implemented under TSMC 40 nm CMOS technology to compare with similar work. The comparison result shows that the proposed HS-LUT gains 6.88% to 51.76% area efficiency improvement.