The following algorithms of RNA secondary structure prediction: the maximum base pairing, Zuker's minimum free energy, the optimal stacking of belieal regions, the random stacking of belieal regions and all possible combinations and the RNA secondary structure drawing based on primary belieal regions have been used to construct RNA secondary structure prediction system named Rnafold. In addition, the former four methods are compared through 20 tRNA sequences in the two aspects of free energy and cloverleaf structure. The statistical difference of free energy was analysed by t-test. From the point of view of cloveleaf structure, the method of randorrT stacking is the best, the second are the optimal stacking and Zuker's algo-rithms and the worst is the maximum base pairing. Finally, the difference between two methods of minimum free energy was analysed.