Bioinformatics analysis of the molecular network regulation is the main content of systems biology, may reveal the complex life phenomena from interactions among molecules and will bring about a far-reaching impact on our current understanding about life activities of organism. MicroRNAs (functional RNAs) can regulate mRNA transcription through inhibition of post-transcriptional protein-coding gene expression, target degradation, etc., and are extensively involved in various biological processes in the cells. It is generally held that the therapeutic effect of acu-moxibustion intervention involves multi-channels, multi-targets, and multi-levels of both peripheral and central nervous systems of the body but has not been fully revealed, being similar with functional forms of molecular regulatory networks. Thus, it is necessary to introduce new ideas and methods for studying the underlying mechanism of acu-moxibustion therapy. The molecular regulatory networks of microRNA would provide a new way for revealing the mechanism of acu-moxibustion interventions.