Heart failure is a complex cardiac disease without effect therapeutic methods, which causes a huge economic and social burden. It is urgent to identify new diagnostic biomarker and develop new therapeutic method. Mitochondria dysfunction is closely associated with the development of heart failure. About 95% ATP consumed by heart are derived from mitochondrial oxidative phosphorylation. The deficiency of myocardial energy supply caused by mitochondrial injury is the key factor linking the mitochondrial dysfunction to heart failure, which involves mitochondrial mediated metabolism disorder, calcium imbalance, oxidative stress, apoptosis and mitophagy. It has been demonstrated that non-coding RNA (ncRNA) playing a critical role in modulating epigenetic modification, post-transcription, translation modification and so on. Many researches showed that ncRNA express abnormally during the heart development and cardiac disease, and exhibit important regulating roles in the regulation of mitochondrial structure and function. Among them, miRNA has been demonstrated widely. Most miRNA, originated from either nuclear or mitochondrial genome, showed important roles in regulating heart pathophysiology change through mitochondrial dysfunction and structure disruption via targeting mRNA or protein. While lncRNA and circRNA play diverse roles in the regulation of mitochondrial structure and function by ncRNA-miRNA-mRNA triple networks, which provide us more perspective to understand the explicit role of ncRNA in mitochondria and heart pathophysiology. However, only a little ncRNA encoded by mitochondrial genome have been confirmed in the process of heart failure. Besides, it is still unclear that how does the ncRNA encoded by nuclear genome transport to mitochondria and vice versa. Moreover, recent studies discovered many other mitochondria encoded ncRNA, such as piRNA and small ncRNA shorter than 200 nucleotides derived from tRNA, rRNA or lncRNA, play important roles in many diseases. It has a broad prospect in investigating the various roles of mitochondria encoded ncRNA. Therefore, this work aims to provide some new ideas and targets for the clinical research and therapy for heart failure via reviewing the newly recent researches about the regulation mechanism of new ncRNAs on mitochondria function in the process of heart failure.