Quantum Cellular Automata (QCA) is an emerging technology at the nanotechnology level. Lower power consumption, higher density and higher speed nature of QCA technology are very interesting. Nowadays, many applications of QCA technology are introduced and cryptography can be an attractive application of QCA technology. The implementation of the Serpent block cipher in Quantum Cellular Automata is the main purpose of this paper. The main modules of this cryptographic algorithm are implemented in this technology and the implementation results are discussed. The two methods of S-Box design, i.e. LUT-Based and Logic-Based methods are inspected. The Serpent's S-Boxes are designed and simulated by these two methods. The simulation results are obtained from QCADesigner software.