The papaya mealybug, Paracoccus marginatus, a significant invasive pest in tropical and subtropical regions, exhibits a notable capacity to withstand high-temperature stress. To elucidate the molecular basis of this thermotolerance, we investigated the role of heat shock protein 90 (Hsp90) genes in this species. The full-length cDNA sequences of three Hsp90 genes—PmHsp90-1, PmHsp90-2, and PmTRAP1—were cloned, subjected to bioinformatic analysis, and their expression profiles under heat stress were detected. RNAi-mediated suppression of PmTRAP1 was conducted to evaluate survival under extreme high-temperature conditions. The open reading frames (ORFs) of PmHsp90-1, PmHsp90-2, and PmTRAP1 are 2175 bp, 2178 bp, and 2085 bp in length, encoding proteins comprising 724, 725, and 694 amino acids, respectively. Phylogenetic and structural analyses confirmed that PmHsp90-1 and PmHsp90-2 are cytosolic isoforms, each containing a characteristic C-terminal MEEVD motif, while PmTRAP1 was identified as the mitochondrial isoform. All three genes were significantly upregulated under heat stress. RNAi-mediated knockdown of PmTRAP1 markedly reduced the survival rate of P. marginatus under extreme high temperature. These findings demonstrate that PmTRAP1 is essential for heat tolerance in the papaya mealybug. This study provides crucial insights into the molecular mechanisms of thermal adaptation in insects and identifies PmTRAP1 as a potential target for future research on managing insect responses to environmental stress.