||Structural DNA nanotechnology uses basic DNA strands, double helical domain and some well-defined sticky ends configurations to construct specific geometrical structures. Various of factors must be considered in DNA motif design, such as crossover location optimization and curvature prevention. It is rather difficult to rely on physical plastic models to design DNA motif. A software that can automatically find a stable state of a specific structure and is capable of generating sequences is essential for progress in the field of structural DNA nanotechnology. In this thesis, A user-friendly software system, UNIQUIMER 3D, was developed. This system has functions for 3D visualization, energy minimization, sequence generation, and construction of motif array simulations (2D tiles & 3D lattices). The system can check the structural deformation and design errors under scaled-up conditions. The system aims to facilitate the design of novel DNA motifs for the DNA nanotechnology. The program has been tested for the design of existing motifs (holiday junction, 4x4 tile, DX, DNA tetrahedron, DNA cube, etc.) The software is provided free of charge to the non-profit research institutions. The software was developed for the Windows environment.