<p>Decapod Iridescent Virus 1 (DIV1) is a recently discovered virus recognized for its high infectivity in <i>Macrobrachium rosenbergii</i>. A thermal treatment was performed on DIV1-infected <i>M. rosenbergii</i>, and the therapeutic efficacy was evaluated. In the DIV1 challenge experiment, the mortality rate in the challenged group was found to be 2.6 times greater than that in the control group, with the viral load in deceased individuals exceeding 5.41×10⁷ copies/μg-DNA. The thermal treatment (TT) was administered at 36 °C for a duration of 16 d, followed by a temperature restoration (TR) period at 26 °C for 3 d. On the first day at 36 °C, an average viral concentration of 5.34×10 copies/μg-DNA was detected in the survived individuals. RNA-seq analysis showed a significant upregulation of genes related to the lysosome pathway, including sialin-like isoform x2 (<i>slc17a5</i>), beta-galactosidase-1-like protein 2 (<i>glb1</i>), putative glucosylceramidase 3 (<i>gba</i>), sphingomyelin phosphodiesterase-like isoform x2 (<i>smpd1</i>), betahexosaminidase subunit alpha-like (<i>hexa_b</i>) and legumain-like protein (<i>lgmn</i>), following a transient suppression period induced by thermal stress. Upon reaching 36 °C, the activation of heat shock protein 70 (<i>hsp70</i>) and heat shock protein 90 (<i>hsp90a</i>) was observed. Concomitantly, genes that implicated in energy production critical for DIV1 replication, such as hexokinase (<i>hk</i>) and microsomal glutathione stransferase 3-like isoform x2 (<i>gst</i>), were inhibited. These results collectively suggest that TT/TR treatments eliminated DIV1 in <i>M. rosenbergii</i> by activating the organism’s innate immune response and suppressing virus replication. This study provides a theoretical basis for utilizing thermal therapy in the management of viral infections in <i>M. rosenbergii</i> breeding programs, thereby facilitating the development of new strains resistant to DIV1.</p>