Neuropeptides and their receptors are involved in the regulation and coordination of various physiological processes in insects.  Although various neuropeptides have been identified previously, the corresponding receptors remain unknown in the oriental fruit fly, Bactrocera dorsalis, an important agricultural insect pest.  It is also unclear whether neuropeptide signaling systems are involved in regulating the thermal tolerance of this notorious pest.  Here, we systematically identified 44 putative neuropeptide receptor genes which encode 66 protein sequences, and analyzed the spatio-temporal expression patterns of the neuropeptide ligands and their receptor genes in B. dorsalis.  We also analyzed changes in their transcript accumulation in two thermo-tolerant populations (heat and cold) of B. dorsalis.  The results showed that numerous neuropeptides and receptors participate in responding to thermal stresses during acclimation.  In particular, the expression of short neuropeptide F (sNPF) was up-regulated in the heat-tolerant population of B. dorsalis.  Moreover, proteomic data showed that sNPF was up-regulated in both thermo-tolerant populations of B. dorsalis.  The functional verification based on CRISPR/Cas9 demonstrated that sNPF is involved in regulating the tolerance to thermal stresses.  The results of this study enrich our knowledge on the function of neuropeptide sNPF in insects.  Moreover, this study demonstrated the role of neuropeptide signaling systems in thermal adaptation, contributing to a better understanding of the rapid invasiveness of B. dorsalis around the world.