Objective. To explore the effect of acupoint application of Chinese medicine on children’s height and bone age. Methods. Altogether, 120 children with a short stature treated in our hospital from September 2017 to September 2018 were divided into the control group (CG, n = 60) and the observation group (OG, n = 60) according to the random number table method. The children in CG were given healthy diet and exercise plans and supplemented with daily vitamin intake. The OG was treated with acupoint application of Chinese medicine on the basis of the CG. The clinical efficacy of the CG and the OG of children after treatment was observed. The height increment, growth rate, and bone age of children were compared before and after treatment. The levels of IGF-1 and 25-(OH)D in the serum of children before and after treatment were tested. According to the clinical curative effect after treatment, the children were divided into good curative effect group (markedly effective + effective) and poor curative effect group (ineffective). Logistics regression analysis was applied to analyze the risk factors. Results. Compared with the CG, the curative effect on the OG was evidently improved ( P < 0.05 ). In addition, the height increment, the growth speed, and the bone age of the OG increased evidently ( P < 0.05 ). Compared with the CG, the expression of IGF-1 and 25-(OH)D of the OG elevated ( P < 0.05 ). Serum IGF-1 and 25-(OH)D concentrations were positively correlated with growth rate and bone age ( P < 0.05 ). Risk factors analysis showed that disease course, IGF-1, 25-(OH)D expression, and heredity were the risk factors affecting the curative effect on children. Conclusion. Acupoint application of Chinese medicine has effect on the height and bone age of children with short stature, which is worthy of clinical promotion. In addition, early treatment should be carried out to improve the clinical efficacy of children.