Gene prediction is a significant task, in which the recognization of exon of eukaryotic gene is a great challenge. In this study, a gene prediction method which is based on 3-periodicity in gene sequences was performed. A more prominent peak value in exon and more steady values in intron were shaped in the power spectrum curves based on arguments of the four bases. The distinction degree of SNR of exons and introns was enlarged and a better effect in short gene prediction was presented. In the condition of threshold R2, the accuracy reached to 94.53%; under the threshold R1, the accuracy reached to 94.50%, and the sensibility reached to 99.45%.