The invention relates to a reactor neutron activation automatic irradiation control system, wherein a P89C669 single chip microcomputer is used as a core, a pneumatic device is controlled to transmita sample to be irradiated into and out of the reactor, a photoelectric detection module is supplemented to precisely control the irradiation parameters of the sample, and communication with a host computer is achieved through a serial interface so as to achieve the integrated control of sample irradiation and measurement. According to the present invention, the irradiation control system adopts the industrial control computer, the single chip microcomputer and the implementing mechanism to form the two-stage control system, such that the precise control of the sample irradiation parameters isachieved, the integrated operation is achieved, and the definite disadvantages that the system generally requires the manual operation and the like are overcome.