The invention provides a method and a device for predicting a ribonucleic acid folding structure containing a pseudoknot based on an extended structure. The method comprises the following steps of randomly inputting one segment of a ribonucleic acid base sequence, defining a pseudoknot and the extended structure, establishing a ribonucleic acid pseudoknot structure characteristic model and a mathematical structure which comprise the pseudoknot and the extended structure, calculating lowest base free energy of the characteristic model, and outputting the ribonucleic acid folding structure whichcomprises the pseudoknot. The device comprises an input unit, an initializing unit, a storage unit, a calculating unit and an output unit. The method and the device realize calculation based on the extended structure. Furthermore continuous stacking and coaxial staking based on the extended structure are introduced, thereby forming an integral and accurate RNA folding structure which comprises the continuous stack, the extended structure, an annular structure and a pseudoknot structure. The searching speed, the accuracy, the sensitivity and the singularity are obviously better than that of prior art. Furthermore the method and the device realize higher effectiveness in predicting the planar pseudoknot and a non-planar pseudoknot structure.