Abstract: Weather modification operation activities are carried out in meteorological departments at all levels extensively. In the traditional operation mode, the command and scheduling information of the prefecture-level weather modification operation are mainly transmitted by telephone, wireless radio, etc. after the command personnel analyzing data manually. The instructions between the command and scheduling personnel are given and fed back mainly in written and oral ways. With the development of social economy and the improvement of the public needs, the scale of the weather modification operation expands rapidly, and the operation becomes more and more frequently. Thus, the traditional telephone and radio communication ways can not adapt to the modernization of the weather business. In order to further improve the work efficiency, the Sanmenxia Weather Bureau has developed a prefecture-level weather modification operation command system based on GIS. The system is consisted of software and hard ware. Thereinto, the command system software uses GIS technology to display the geographic information of operation areas, and obtains radar maps, satellite cloud pictures and so on, after a series of data processing to provide data support for the decision of the operation commander’s. The software will generate detailed operating parameters for the operating personnel at the short point according to the pre-established conditions automatically, and transfer the operational instructions to command operation display screen by short message, electronic screen, voice speaker and send them to the front-line operation personnel. The system mainly includes the geographic sand table model as command auxiliary and mobile phone, voice speaker, LED electronic screen, etc as the instruction receiving terminal. The instruction receiving program connects to the system server through the GPRS network. The system has been applied in the meteorological department of the counties in the districts of Sanmenxia already. It has been functioning stably and reliably as well as receiving instructions timely and accurately. It turns out to reach the expected design purpose.