Abstract: Disclosed is a visualization method of RNA pseudoknot structures. The method of the invention comprises the steps of setting criteria required for visualizing RNA pseudoknots, setting structural elements and data structures for representing a whole RNA structure containing pseudoknots, determining an input format for visualization and a drawing order of the structure, determining connectivity relations between regular loops and stems in the structure and between pseudoknot loops and stems in the structure, calculating radii of the regular loop and the PK loop, calculating coordinates of bases in the regular loops, setting internal angles of the PK loops, calculating startAngles of the regular loops and angles of the stem, determining positions of the pseudoknots in the PK loops, and drawing the pseudoknots and the whole RNA structure containing the pseudoknots.