The invention discloses an unmanned-aerial-vehicle-based blue-green algae monitoring and early-warning method and system. The method comprises: (10), carrying out general investigation of a monitored water area; to be specific, collecting millimeter-wave radiation data on the way and blue-green algae location information; (20), carrying out contaminated area imaging; to be specific, carrying out key-point conical scanning to obtain a radiation image and shooting an optical image; (30), carrying out image feature extraction; to be specific, carrying out processing on the radiation image, carrying out a contrastive analysis on the processed radiation image and the optical image, and carrying out real-time monitoring; and (40), carrying out early warning of blue-green algae pollution; to be specific, determining blue-green algae pollution and generating blue-green algae pollution early warning. In addition, the system consists of an unmanned aerial vehicle monitoring platform (1) and a ground console (2) that are in remote wireless network signal connection. The unmanned aerial vehicle monitoring platform (1) carries out general investigation, detailed fixed-point investigation, and real-time monitoring on a monitored water area; and the ground console (2) controls the unmanned aerial vehicle monitoring platform (1) to determine a polluted water area, extract an image feature, and generates blue-green algae pollution early waning. The monitoring and early-warning method and system have advantages of all-time and all-weather working and high monitoring precision.