Understanding the variations in gene expression between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques and crab-eating macaques serve as crucial nonhuman primate biomedical models with different phenotypes, but the large-scale of comparative transcriptome research between these two species has yet to be fully elucidated. Here, we conduct systematic comparisons utilizing newly sequenced RNA-seq data from 84 samples (41 Mfa samples and 43 Mmu samples) encompassing 14 common tissues. Our findings reveal that a small fraction of genes (~3.7%) show differential expression between the two macaque species, while ~36.5% of genes show tissue-specific expression in both macaques. We also compare gene expression between macaques and humans and ~22.6 % of the orthologous genes show differential expression in at least 2 tissues. Moreover, ~19.41% of genes overlapped with macaque-specific structural variants are more likely to show differential expression between humans and macaques. Of these, FAM220A shows elevated gene expression in humans compared to macaques because of lineage-specific duplication. In summary, our study presents a large-scale analysis of the transcriptomes within macaque species and between macaques and humans. These insights into gene expression variations will enhance the biomedical utility of macaque models and contributing to the broader realm of primate genomic studies.