The content of mineral elements in Chinese herbal medicines is an important indicator for the quality evaluation of Chinese herbal medicines and is closely related to the growth and development, the formation of functional substances and the efficacy. The content and proportion of mineral elements vary with origin, harvest time, and harvesting parts, but the germplasm is the stablest and most important factor influencing the content and proportion of mineral elements in Chinese herbal medicines. Inductively coupled plasma atomic emission spectrometry (ICP-AES) can rapidly and simultaneously determine a variety of mineral elements. It has been widely used in the determination of mineral elements in Chinese herbal medicines. Cistanche deserticola is a famous tonic herbal and its mineral element content and proportion have attracted more and more attention. In this study, using C. deserticola germplasm of different flower colors as materials, the mineral element K, P, Ca, Mg, Na, Fe, Mn, Zn, Cu and Mo in C. deserticola germplasm of different flower colors were determined by ICP-AES method after the materials digestion with nitric acid and perchloric acid. The results show that: (1) The germplasm affected the content of mineral elements in C. deserticola. C. deserticola germplasm of different flower colors were rich in K, P, Ca, Mg, Na, Fe, Mn, Zn, Cu, Mo, but with significant differences. (2) The content and accumulation of K in C. deserticola germplasm of different flower colors were the highest among macroelements. Especially, the content and accumulation of K in C. deserticola germplasm of the white color flower reached 15.91 mg·g-1 and 727.76 mg·plant-1. The content and accumulation of P in C. deserticola germplasm of different flower colors were the lowest among macroelements. The content and accumulation of P in C. deserticola germplasm of the lavender color flower were 0.45 mg·g-1 and 21.8 mg·plant-1. (3) The content and accumulation of Fe in C. deserticola germplasm of different flower colors were the highest among microelements. Especially, the content and accumulation of Fe in C. deserticola germplasm of the yellow color flower reached 722.33 μg·g-1 and 30 251.29 μg·plant-1. The content and accumulation of Mo in C. deserticola germplasm of different flower colors were the lowest among microelements. The content and accumulation of Mo in C. deserticola germplasm of the lavender color flower were 0.11 mg·g-1 and 5.12 mg·plant-1. (4) The content and accumulation of K, Ca, Mg, Mn, Zn were with higher values in C. deserticola germplasm of the white color flower, while the content and accumulation of K, Ca, Mg, Na, Mn were with lower values in C. deserticola germplasm of the lavender color flower. (5) The germplasm affected the proportion of mineral elements in C. deserticola. The proportion of mineral elements in C. deserticola germplasm of different flower colors were different. The proportion of K∶P and Fe∶Mn were with significant differences, while Ca∶Mg and Zn∶Cu were with little differences. Conclusion: C. deserticola was rich in mineral elements, and the germplasm affected the content, accumulation and proportion of mineral elements in C. deserticola and there are significant differences among different flower colors. The results should be concerned about and paid attention to. Mineral elements are important indicators for the quality evaluation of Chinese herbal medicines and affect the growth and development. Therefore, the results of this study could provide the basis for quality evaluation, nutrition evaluation and scientific fertilization of C. deserticola germplasm of different flower colors.