The screening experiment of 20 medicinal plants was performed to check the effect on height growth. As a result, aqueous extracts of Cornus officinalis, Zizyphus jujuba and Dioscorea batatas were shown to be effective. This study, each marker compound (loganin, jujuboside A, and dioscin) was set up the selected three plants and high-performance liquid chromatography (HPLC) was used for the method validation and quantitative analysis of extracts. Extractions from Cornus officinalis, Zizyphus jujuba and Dioscorea batatas were performed with a reflux method using 100% water as a solvent. Parameters such as linearity, specificity, precision and accuracy were performed for the validation of HPLC analysis methods. Correlation coefficient of calibration curves in all three marker compounds was shown to be higher than 0.9994. The ranges of limits of detection (LOD) and limits of quantification (LOQ) were from 1.43 to 4.04 mg/L and 1.33 to 7.182 mg/L, respectively. Accuracy of intra-day and inter-day ranged from 80 to 120% and precision ranged from under 15%. It was found that Cornus officinalis, Zizyphus jujuba, and Dioscorea batatas contained 0.81% of loganin, 24.23% of jujuboside A, and 0.015% of dioscin, respectively by the validated analysis method. These results can provide analysis conditions for three marker compounds and can be used as quantitative analysis. This study can be applied to fundamental data for herbal medicines to promote height growth using Cornus officinalis, Zizyphus jujuba and Dioscorea batatas.