Many kinds of physical field are able to affect the biological activity, such as electromagnetic field, magnetic field, scalar wave, magnetic vector potential and so on. Some works investigated a high-penetrating emission (HPE) generated by a LED generator that can affect the conductivity of water and the growth of dry yeast. In this research, the biological effect of the HPE of LED generator on S. cerevisiae was studied. The results showed that this kind of HPE could promote the growth of S. cerevisiae. With the decrease of initial concentration and the extension of exposure time, the growth promoting effect of HPE increased significantly. When the initial cell concentration was 2 × 102 cell/ml and exposed for 24 h, the number of yeast cells increased by 19.5% compared with the control group. Further studies showed that adenosine triphosphate (ATP) content and the ratio of ATP and adenosine diphosphate (ADP, ATP/ADP ratio) of exposed cells were higher than those of unexposed cells, indicating that exposed cells had higher cell viability and energy status. In addition, the intracellular superoxide (O2−) content decreased significantly after the HPE exposed. In this study, the stainless steel box acts as a Faraday cage to shield the electromagnetic field, so the biological effect of the HPE is not produced by the electromagnetic field. Nevertheless, the mechanism of the HPE is still unknown and needs further research. This is the first report on the effect of HPE on mitochondrial parameters, contributing to further study on HPE and revealing potential for future medical applications.