The invention discloses an on-site epidemiology intelligent investigation system. The system is composed of a handheld mobile terminal and a server, wherein the handheld mobile terminal and the server are interconnected via a network; the handheld mobile terminal is a mobile working application carrier, comprises a one-dimensional and two-dimensional code scanning and communication interface and a data line interface, and further comprises the following functional modules: a data display module, a data acquisition module, a graphic image acquisition module, a data local storage module and a wireless communication functional module; and the server comprises an application server, a data server and a file server, and further comprises the following functional modules: an epidemic situation management module, a knowledge base management module, a disease monitoring management module, a system management module and a forum management module. Users can choose to use a PC (Personal Computer) terminal mode or a handheld mobile terminal mode for data acquisition and query works according to site conditions, the data is transmitted in a wire transmission form or wireless transmission form, the use flexibility and compatibility of the system can be ensured, and the system exerts the effects of practical investigation works to the greatest extent.