Mitochondria are semi-autonomous cellular organelles responsible for oxidative phosphorylation (OXPHOS) and adenosine triphosphate (ATP) synthesis and are the powerhouses of cellular metabolism. Mitochondria are present in almost all eukaryotic organisms and are involved in apoptosis, calcium homeostasis, and regulation of the innate immune responses, which play a vital role in normal physiological processes. Mitochondria contain their own DNA that encodes 37 genes, including 2 rRNAs, 13 mRNA, and 22 tRNAs genes. Gene expression in mitochondria involves complex transcriptional and post-transcriptional processes, including cleavage of polycistronic RNA, RNA modification, and terminal processing of RNA. These processes require the coordinated spatiotemporal action of several enzymes, and many different factors are involved in the regulation and control of protein synthesis to maintain the stability and turnover of mitochondrial RNA. Disorders in mitochondrial RNA processing lead to changes in RNA expression profiles, interfere with protein translation, cause mitochondrial dysfunction, and result in a variety of mitochondria-related diseases. Although substantial progress has been made in the field of mitochondrial RNA processing and regulation, there are still many controversies and unknowns. This article reviews the latest research progress on mitochondrial DNA transcription, RNA post-transcriptional processing, and factors affecting RNA processing.