Qigong is a traditional method of exercise in China and is effective in maintaining physical and mental health, and even in curing diseases. There are many reports about the beneficial effects of Qigong while the underlying functional mechanism has not been systematically explored at the molecular and cellular levels. In this study, we examined the effect of Qigong on gene expressions of mouse M-1 cells using the quantitative real-time polymerase chain reaction (qRT-PCR) and the transcriptome sequencing technology. Analysis result showed that several genes were upregulated the expression level related to cell proliferation and apoptosis by Qigong treatment. Enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) of differentially expressed genes (DEGs) showed that DEGs are related to many important signaling pathways in cells such as PI3K/AKT, and up-regulated DEGs are beneficial to cell growth, resistance to oxidative damage and apoptosis in vitro. Our study provided some important molecular insights into the positive effect of Qigong, which will help to comprehensively understand the biological mechanism of Qigong on human health and promote the application of Qigong treatment and the related research.