The invention discloses a method for SNP locus predicting and influencing the biological function of long non-coding RNA. The method firstly establishes the recognition and significance evaluation method of the specific motif sequence which can be identified by the RNA binding protein contained in the long non-coding RNA, and then evaluates the influence caused by the SNP locus in the specific sequences based on the method. By using the method, SNP locus with important influence on the biological function of the long non-coding RNA can be found, reliable functional research leads are providedfor experimental personnel, and guidance is also provided for clinical application of long non-coding RNA.