The possibility of remotely manipulating intracellular pathways in single cells is one of the current goals of regenerative medicine, which requires new strategies to enhance tissue repair and reprogram stem cell activity. Due to the improved controlled synthesis that allows for convenient adjustment and precise thermal positioning, plasma nanomaterials are meeting this demand. By utilizing the thermal properties of gold nanoprisms (AuNPs) and the unparalleled regenerative ability of small invertebrate Hydra vulgaris, the molecular mechanisms behind animal regeneration can be demonstrated by using AuNPs and applying conventional pulses of near-infrared radiation (NIR). AuNP light stimulation improved head regeneration efficiency, reproductive ability, and stem cell proliferation rate, indicating that near-infrared induced hyperthermia is a new tool for enhancing tissue regeneration. By transcriptome analysis of key developmental genes in animals exposed to external heat or radiation, an estimate of the heat generated by intracellular nanoheaters in vivo was obtained, revealing Hydra as a live thermometer for testing the properties of plasma materials. These results reveal a new function of thermogenic nanoparticles, which controls cell stemness by activating a molecular pathway that can serve as a target for regenerative medicine or wound healing strategies.