The present invention relates to a visualization method of RNA pseudoknot structures for more efficiently and clearly visualizing all types of RNA pseudoknot structures including H-types in the form of a planar graph without edge-crossing so that the structures can be easily examined. The visualization method comprises reading the structure data in bracket view, identifying stem-loops and pseudoknots enclosed in bracket pairs from the input structure data, first computing the position and shape of a stem-loop contained in an identified pseudoknot to visualize the stem-loop, second computing the position and shape of the pseudoknot containing the calculated stem-loop to visualize the pseudoknot, third computing the position and shape of a stem-loop outside the computed pseudoknot, and inserting or connecting the visualized stem-loops into or to the pseudoknots to complete an RNA pseudoknot structure drawing.