Abstract Precise regulation of medium and micronutrients is vital for medicinal plant cultivation and quality improvement, yet requirements of these nutrients in Epimedium pubescens growth are unclear. This study monitored the annual dynamics changes in the content of seven medium and micronutrients within E. pubescens leaves; and identified key nutrients affecting growth through nutrient deficiency experiments. Variance Partitioning Analysis (VPA) was utilized to quantify stage-specific contributions of these key nutrients to biomass accumulation and Icariin-Flavonoids (I-Fla) synthesis. Results revealed significant temporal dynamics in leaf mineral elements, with abundance ordered as Ca > Fe > Mg > Mn > Zn > Cu > Mo. Notably, the high accumulation of Fe (a micronutrient) may indicate species-specific demand. Nutrient deficiency experiments confirmed Mg, Fe, and Zn functioned as core elements governing growth, with deficiency causing chlorophyll loss and biomass reduction. Specifically, Mg emerged as the dominant contributor to biomass accumulation, particularly in April (62.4%) and July (61.2%); a pronounced synergistic effect between Fe-Zn was observed, showing a consistent contribution rate exceeding 10% to biomass throughout the growth period. For I-Fla, Mg exerted significant effects in February (44.2%), whereas Zn's contribution progressively increased (July: 23.3%; next February: 44.5%), underscoring its pivotal regulatory role in secondary metabolism. The study proposed a range for key medium and micronutrients with a fertilization scheme: Mg reinforcement (Feb-Apr, Jul); Fe-Zn supplementation (Jul); and Zn prioritization post-Oct. It elucidated medium and micronutrients dynamics in E. pubescens and their relationships with growth and I-Fla synthesis, establishing the nutritional basis for coordinated yield-quality improvement. These findings provide a theoretical framework for precision cultivation and sustainable development of medicinal plants.