A comparative analysis is made of the droughts over the Urumqi River basin using the observation data from the Yingxiongqiao hydro station and Urumqi meteorological station. The data series from 1960 to 2010 is used to calculate the Standardized Precipitation Index (SPI) and Z index both in the mountainous and plain areas of the Urumqi River basin, and the data of historical drought events are used to validate the results. Results indicate that for the plain area drought indexes calculated by the data of the Urumqi meteorological station from 1960 to 1978, the values of SPI and Z index are negative, meaning that the drought condition stayed in a near normal or dry level; after the year of 1978, the values of SPI and Z index began to grow with a fluctuation, with the trend of a nondrought or near normal level. For the Yingxiongqiao hydro station, the values of SPI and Z index from 1960 to 2010 showed a fluctuation with the near normal level as a main characteristic. The consistency of SPI and Z indexes indicates that drought levels changed in a very same pattern and the two curves of SPI and Z index matched very well. In terms of the mountainous and plain areas, before the year of 1978, the drought level of mountainous area was less than that of the plain areas, and after the 1978, the mountains areas had higher levels of droughts than the plain areas. The seasonal change of droughts is mainly characterized by moderate dry and occurred in summer and fall, and the severe and extreme droughts had less occurrence probability than moderate droughts, mainly happening in spring and fall. Validation shows that SPI and Z indexes are applicable to the investigation of drought patterns in the study area.