Abstract: As an important feature in the macroscopic characteristics of clouds, the vertical structure characteristics of clouds determine different types of clouds and affect the energy budget balance of the earth’s atmosphere system through absorbing and emitting radiation. Therefore, research about the vertical structure characteristics of clouds is always an important subject of cloud physics. As an instrument for observing the vertical structure characteristics of clouds, a sounding balloon can penetrate clouds to achieve temperature and humidity profiles in high resolution. Based on this information, the vertical structure of the clouds can be precisely identified using some methods. This paper uses the observation data of national operational radiosonde sites to identify the vertical structure of the clouds by the relative humidity threshold method, and tests the cloud boundary by comparing it with the data from the ceilometer and “FengYun-4” satellite. Based on this, the mean vertical distribution of one-, two-, and three-layer clouds is obtained from 2015 to 2017 and analyzed in daily, seasonal, and regional variations. The results indicate that (1) one-layer clouds are generally located at altitudes between the altitudes of the two- and three-layer cloud configurations. With the increase of the number of cloud layers, the uppermost layer becomes higher and the lowest layer becomes lower. (2) In the diurnal variation, the lowest cloud base height of single and multilayer clouds at noon is higher than those in the morning, and the uppermost cloud top height of single and multilayer clouds in the evening is higher than those in the morning and at noon. The variation of the mid layer in multilayer clouds is less than that in the uppermost and lowest layers. (3) In the seasonal variation, there are more clouds that are more vertically developed during summer than other seasons, suggesting that the development of clouds is favorable under warm atmospheric conditions. (4) The regional variation of the vertical cloud distribution in China shows an obvious latitudinal variation trend. Thin clouds with a higher cloud base centered on the Tibetan Plateau in the southwest gradually transform to thick clouds but with a lower cloud base in the coastal area of the southeast. This indicates that different cloud types are directly affected by different geographical conditions and climate zones.