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Brown adipose tissues have unique non-shivering thermogenesis functions, can be found in newborn ruminate animals, and then are gradually replaced by white adipose tissues in adulthood. For the purpose of exploring the intrinsic mechanism underlying the conversion process from brown (BAT) to white adipose tissue (WAT), it is necessary to utilize Quantitative PCR (qPCR) to study gene expression profiling. In this study, we identified reference genes that were consistently expressed during the transformation from goat BAT to WAT using RNA-seq data. Then, twelve genes were evaluated as candidate reference genes for qPCR in goat perirenal adipose tissue using three tools (geNorm, Normfinder, and BestKeeper). In addition, the selected reference genes were used to normalize the gene expression of <i>PGC-1α</i> and <i>GPAT4</i>. It was found that traditional reference genes, such as <i>GAPDH</i>, <i>RPLP0</i>, <i>HPRT1</i>, and <i>PPIA</i> were not suitable for target gene normalization. In contrast, <i>CTNNB</i>, <i>PFDN5</i>, and <i>EIF3M</i>, selected from RNA sequencing data, showed the least variation and were recommended as the best reference genes during the transformation from BAT to WAT.