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Simple Summary: Arylalkylamine N-acetyltransferase (AANAT) is an enzyme that regulates the production of melatonin, a hormone that is essential for organisms to maintain circadian and annual rhythmic behavior. The AANAT gene has undergone gene duplication and inactivation during evolution. Nevertheless, the majority of mammals retain a solitary copy of AANAT within the biological genome, and the mechanisms by which this gene responds to environmental stimuli remain poorly understood. To address this issue, we investigated the adaptive evolution of AANAT at both the gene and protein levels. Our study revealed the presence of multiple mutation sites within the gene encoding AANAT, with variation in the structure of the AANAT protein observed across different geographic populations. We identified a positive selection of AANAT in populations residing at higher latitudes. Furthermore, individuals exhibiting longer hibernation periods displayed significantly higher catalytic efficiency of the AANAT enzyme compared to those with minimal hibernation behavior, suggesting a potential association between AANAT and hibernation rhythms. This study adds to our understanding of the adaptive evolution of AANAT and may provide molecular evidence for hibernation rhythm adaptation in bats. Arylalkylamine N-acetyltransferase (AANAT) is a crucial rate-limiting enzyme in the synthesis of melatonin. AANAT has been confirmed to be independently duplicated and inactivated in different animal taxa in order to adapt to the environment. However, the evolutionary forces associated with having a single copy of AANAT remain unclear. The greater horseshoe bat has a single copy of AANAT but exhibits different hibernation rhythms in various populations. We analyzed the adaptive evolution at the gene and protein levels of AANAT from three distinct genetic lineages in China: northeast (NE), central east (CE), and southwest (SW). The results revealed greater genetic diversity in the AANAT loci of the NE and CE lineage populations that have longer hibernation times, and there were two positive selection loci. The catalytic capacity of AANAT in the Liaoning population that underwent positive selection was significantly higher than that of the Yunnan population (p < 0.05). This difference may be related to the lower proportion of α helix and the variation in two interface residues. The adaptive evolution of AANAT was significantly correlated with climate and environment (p < 0.05). After controlling for geographical factors (latitude and altitude), the evolution of AANAT by the negative temperature factor was represented by the monthly mean temperature (r = −0.6, p < 0.05). The results identified the gene level variation, functional adaptation, and evolutionary driving factors of AANAT, provide an important foundation for further understanding the adaptive evolution of the single copy of AANAT in pteropods, and may offer evidence for adaptive hibernation rhythms in bats. [ABSTRACT FROM AUTHOR]