The invention relates to a system screening and clone identification method for heat shock protein genes of agasicles hygrophila and belongs to the technical field of gene engineering. The method comprises the steps that larvas of one to three ages, pupas of 2-6 days of age and imagoes which are subjected to eclosion in one day are taken, and the treatment samples above are collected and frozen for storage in liquid nitrogen; overall-length cDNA segment of mRNA is synthesized, an overall-length cDNA segment is screened, and cDNA gene banks different in capacity are established; the screened overall-length cDNA is subjected to secondary PCR amplification; the tail end of the overall-length cDNA is repaired; then secondary screening is conducted, and a testing gene bank is obtained; after the gene bank is established, the capacity of the gene banks is detected, after the gene bank quality detection result reaches the demand, on-computer sequencing is conducted, obtained non-redundant transcript sequences are compared with NR, Swissprot, GO, COG, KOG, Pfam and KEGG databases, annotation information of a transcript is obtained, all the heat shock protein genes are screened, EST sequence groups of each piece of heat shock protein are spliced and assembled, the most complete gene sequence is obtained, and finally according to the complete sequence, a primer is designed, and clone sequencing is conducted.