This paper addresses the spatial and temporal variation of cloud cover at different heights over southern China and its relationship with precipitation, which is useful for understanding the role of clouds in precipitation and feedback mechanisms as well as provides a basis and foundation for the development of cloud water resources. Based on 12 years (1998-2009) data from the D dataset of International Satellite Cloud Climatology Project (ISCCP), the temporal and spatial distribution characteristics of total cloud cover, low cloud cover, medium cloud cover and high cloud cover were analyzed over Southern China. And based on the CMORPH-AWS merged gridded precipitation product which combined National Oceanic and Atmospheric Administration (NOAA) Climate Prediction Center (CPC) morphing technique (CMORPH) with precipitation observations from automatic weather stations, the relationships between the cloud cover and precipitation intensity, precipitation frequency were analyzed over southern China. The results are as follows: (1) The spatial distribution of total cloud cover and medium cloud cover over southern China was similar. The high-value center was located over the junction of Sichuan Basin, Guizhou and Chongqing, while the low-value center was located in Yunnan. High clouds were distributed in the western part of southern China, and decreased from west to east. Low clouds were mainly distributed over the southeastern part of southern China. Overall, low cloud cover decreased from coastal area to inland area. (2) The seasonal variation of total cloud cover and high cloud cover was similar, with cloud cover more in summer and less in winter. Moreover, the high value center of total cloud cover shifted with the seasons. The high cloud cover changed seasonally. The moderate cloud cover and low cloud cover were more in winter and less in summer, with small seasonal changes. (3) With the increase of total cloud cover and high cloud cover, the precipitation intensity increased but the monthly precipitation frequency decreased. With the increase of medium cloud cover, the frequency of monthly precipitation increased, while effect on precipitation intensity varied little. (4) With the increase of cloud cover of stratocumulus and stratus clouds, precipitation intensity and monthly precipitation frequency decreased. With the increase of cloud cover of altocumulus, altostratus and deep convection clouds, precipitation intensity increased while monthly precipitation frequency decreased. In general, cloud cover and precipitation were closely related over southern China, especially total cloud cover and high cloud cover had a greater influence on precipitation intensity and precipitation frequency, while medium cloud cover only had a greater impact on precipitation frequency. The cloud cover of stratocumulus, stratus, altocumulus, altostratus, deep convection clouds had a greater influence on precipitation intensity and precipitation frequency, while cloud cover of cirrus and cirrostratus only had a greater impact on precipitation intensity.