The invention discloses a corn lncRNA screening and classifying method based on an ARM processor. The method comprises the following steps that firstly, a full-length cDNA sequence of corn is input into a CPLD; secondly, a cDNA sequence with the length larger than 200 is screened out, open reading frame prediction is carried out on cDNA, a threshold is determined, the cDNA with the length smallerthan the threshold is determined, the cDNA is in homologous comparison with known protein, non-homologous parts are reserved, secondary structure prediction is carried out on existing plant lncRNA, secondary structure features are extracted, meanwhile, secondary structure prediction is conducted on remaining sequences, the part meeting the structure features is reserved, the to-be-screened cDNA sequence is compared with the small RNA sequence, and a small RNA precursor is removed; thirdly, the corn lncRNA sequence with the known function is collected, structure prediction is conducted, structure feature extraction and screening are conducted on the functional lncRNA, known functional corn lncRNA structure feature sets are constructed, secondary structure extraction is conducted on the cornlncRNA screened out in the second step, the structure feature sets are compared, and lncRNA functions are confirmed and classified.