Background: Domestic donkeys (Equus asinus) are farm animals; they are used mainly for carrying loads in the past centuries. Recently, interests on donkey milk and meat production have increased in many countries. Donkey meat is extremely popular in China due to its high nutritional value and unique flavor. Except the origin and domestication of donkeys, few genetic studies have been conducted. Moreover, data from transcriptional profiling and microRNA (miRNA) regulation of skeletal muscle tissues in donkey are scarce. Recent developments in high-throughput sequencing techniques can offer large-scale analysis of gene expression in different species. This study aimed to explore the differences of the molecular and regulation mechanisms among donkey meat, beef, and mutton using genome-wide transcriptomic analysis and proteomic methods to provide more effective genetic information.Methods: RNA sequencing and proteomic analysis (on the basis of isobaric tags for relative and absolute quantitation) on donkey, cow, and goat muscles, and miRNAs in donkey muscles were detected. We performed a comprehensive research on total RNA, including miRNAs from donkey muscles. The mRNA expression profiles were characterized and differences in single-copy homologous genes among species were analyzed.Results: Most differentially expressed genes were associated with pathways related to protein and fat synthesis and metabolism, muscle formation, and development. We identified single nucleotide polymorphisms (SNPs) in donkey muscle and alternative splicing (AS) events. A total of 57,201 putative SNPs were found, and the main SNP variations were located in known genes. Several AS events occurred in genes related to muscle fiber. Different AS events were also noted among species. Muscle proteomic data were obtained, including all expressed proteins and differentially expressed proteins. Combined transcriptomic and proteomic analysis effectively revealed pivotal mRNAs and proteins in muscles. We found five genes associated with thin and thick filaments, which indirectly explained the characteristics of donkey muscle fibers.Conclusion: RNA-seq and iTRAQ analysis revealed altered expression of genes and proteins in three kinds of muscle. In the highly expressed genes of donkey muscle, we discovered 31 expressed genes were involved in muscle contraction and skeletal muscle fiber development. Compared with mutton, five genes related to muscle fiber synthesis were found and showed differences both at transcriptional and proteome levels in donkey muscle. Meanwhile, genetic variation and regulatory factors can combine as a database to provide more valuable molecular information for further analysis.