The invention discloses an accelerator beam cross section measurement system based on LabVIEW. The accelerator beam cross section measurement system comprises a fluorescent target, an observation window, a transmission system, a grating ruler and an electronics processing module thereof, a camera, a switch and an upper computer; the transmission system comprises a transmission rod, a transmission mechanism, a servo motor, a servo motor driver and a motion controller; the fluorescent target and the camera are driven by the transmission system to do linear motion; the camera is connected with the switch through a network cable, and the switch is connected with the upper computer through the network cable again; real-time position information of the fluorescent target is obtained by adopting the grating ruler and then converted into a network signal by using the electronics processing module of the grating ruler, and the network signal is transmitted to the upper computer for processing. The invention further discloses an accelerator beam cross section measurement method based on LabVIEW. The accelerator beam cross section measurement system disclosed by the invention has the advantages of being high in signal bandwidth, good in real time and high in stability, the measurement accuracies of the cross section size and the position of a beam reach 0.1 millimeter respectively, and the image transmission distance reaches 100 meters.