DNA methylation may play a vital role in tissue development and differentiation as it plays an important role in gene expression regulation. In previous studies, epigenetic variation in the muscles of bat populations were explored; however, the extent of the patterns and levels of genomic DNA methylation among tissues in chiropteran animals have yet to be investigated. In this study, the epigenetic variation of six tissues in normal state Rhinolophus ferrumequinum (i.e., no pregnancy, nursing, or hibernation) was explored using the F-MSAP technique, including brown adipose tissue (BAT), brain (B), heart (H), kidney (K), liver (L), and muscle (M) tissues. An average of 67.0% CCGG loci was methylated in each tissue. There were significant methylation differences among tissues in full-methylation (p < 0.001) and total methylation (p = 0.001). Moreover, various unique methylated loci (15–59) were also detected. Non-negligible level of hemi-methylation (31.4%) existed, indicating that CHG methylation may also play a potential role in tissue development and differentiation in R. ferrumequinum. BAT and B had different methylation profiles compared to the other four tissues, but the underlying mechanism for this requires further investigation. This work provides basic data for future studies on the intrinsic epigenetic mechanisms of vital biological processes, such as tissue development and differentiation, hibernating processes, and the environmental adaptability of Chiropteran animals.