With the development of international trade and frequent personnel exchanges, biological invasion is showing a rapidly growing trend worldwide. Insects are ectothermic animals, so their geographical distribution is due largely to their high and low temperature tolerances. To study the temperature response mechanisms of Bemisia tabaci MED cryptic species, miRNA-seq technology was used to unravel the miRNA library of B. tabaci MED in three field populations (TP, HB, and HK) from cities with different environmental temperatures. We identified 12 differentially expressed miRNAs in response to temperature stress, and Bta-miR-998 and Bta-miR-129 were shown to be associated with temperature tolerance. In addition, we predicted and verified the target genes associated with the temperature tolerance imparted by Bta-miR-998 and Bta-miR-129. The results showed that the down-regulated target gene of Bta-miR-129, BtMGAT3, significantly reduced the heat tolerance and another down-regulated target gene, BtRGS7, affected the cold tolerance of B. tabaci MED. These results indicate that gene expression regulated by miRNAs is an important temperature response mechanism in B. tabaci MED. This study reveals the important regulatory role of miRNA in insect temperature adaptation and provides a new avenue for studying the regulation of insect gene expression by miRNA.