With rainfall changes, hydrological process variability increases. This study predicts the potential effects of temperature and topography characteristics on rainfall spatial variability. Temperature and topography were considered as two effective factors that may influence monthly rainfall. This study uses rainfall and temperature data from 174 synoptic and climatic stations and 39,055 rain, elevation and temperature points extracted by ArcGIS10.3 over the 40 years (1975–2014). In this study, in order to predict the relationship between temperature, topography and rainfall, a combination of statistics including spatial statistics and Geographical information System (GIS) methods were employed. It was found that the distribution and rainfall variability in some parts of Iran was regarded to be based on topography and temperature. The spatial patterns showed that the variability based on spatial autocorrelation in rainfall severity gradually increased from west to east and north to south in Iran. Temperature and topography influence rainfall spatial variability; moreover, these factors have direct, indirect and total effects on rainfall variability in temporal and spatial patterns. These research results will be useful for the regionalization of climate and rainfall formation factors, management of water sources, environmental planning and measuring environmental controls on the climate system.