As a traditional herbal medicine, the clinical efficacy of Ganoderma lucidum (G. lucidum, also known as Lingzhi in China) has been proved by clinical research and a large number of animal experiments. However, its pharmacological mechanism is not clear. Here, we used the Caenorhabditis elegans as an animal model to study the anti-oxidative stress and anti-aging effects of G. lucidum water extract. Our results showed that G. lucidum effectively promoted the nematodes to resist the oxidative stress of paraquat and heavy metal Cr6+, and significantly prolonged the lifespan of the nematodes. The underlining mechanisms were further investigated by focusing on the signaling pathways that regulate the stress responses and the lifespan. We found that G. lucidum protected the nematode against the insults of paraquat and heavy metals through the diet restriction pathway and the mTOR/S6K signaling pathway, respectively. Whereas, the effect of G. lucidum on the longevity of the nematode mainly depended on the germline signaling pathway. Microarray assays were conducted to reveal the gene expression profiles. The expression levels of 2746 genes were significantly changed during the aging process, of which 34 genes were reversed in their expression by the treatment of G. lucidum in aged nematodes. These results suggest that G. lucidum regulates the biophysiological processes in the nematodes through multiple signaling pathways.