Epimedium pubescens, a shade-tolerant medicinal plant, currently faces supply shortages. To investigate the regulatory mechanisms of shading intensity on its growth and quality, this study established four treatments under a Phoebe zhennan plantation: inter-row artificial shading (0% shading, S-0; 50% shading, S-50; 75% shading, S-75) and natural canopy shading (S-93). When monitoring environmental factors, photosynthetic parameters, biomass, and total flavonol glycoside content, significant differences among treatments were only observed regarding solar radiation. Compared with inter-row treatments, S-93 reduced the maximum net photosynthetic rate and per-plant biomass by 33%–86% and 35%–71%, respectively. Structural equation modeling revealed that understory radiation indirectly influenced yield by regulating the vapor pressure deficit and net photosynthetic rate (R² = 0.95). Economic assessments, based on hectare-scaled yield (converted from plot units) and input costs (seedlings, land rental, labor), indicated that the 75% inter-row shading treatment applied from July to October (S-75) was optimal, generating a net annual income of 56,924.5 USD·ha⁻¹. This study provides a theoretical basis for the understory cultivation of E. pubescens.