Understanding the adaptive evolution of species has long interested evolutionary biologists. Adaptive phenotypes can result from changes in protein-coding sequences that affect protein structure and function. The Rhinolophus macrotis group as a specific group has low echolocation frequency relative to body size compared with other rhinolophids, suggesting a special evolutionary process of this group. Transcription bridges genetic information and phenotypes. Here, we sequenced transcriptomes of the brain, liver, and cochlea for five species of the macrotis group and its closely related species, R. pusillus, to explore the molecular basis of the adaptation in the macrotis group at the sequence level. Strong and significant positive selection signals for species within the macrotis group was detected in seven genes (CRYM, FOXM1, MAP6, PYCARD, SLC35A2, WRB and SPRY2) linked to hearing. Unexpectedly, we also detected five PSGs (ARRDC3, LZTFL1, RAB8A, IGFBPL1 and TRNT1) linked to vision in species with relatively low frequencies. These results suggested that natural selection has led to the positive selection of some sensory-related genes. Furthermore, PSGs identified in the macrotis group significantly enriched in GO categories related to metabolism (e.g. catalytic activity and oxidoreductase activity), which provided evidence to parse the genetic adaptations of the species with low frequencies within the macrotis group. This is the first attempt to detect genome-wide sequence evolution across the macrotis group and our study provided valuable resources for studying the genetic mechanisms of rhinolophids adaptation.