The invention relates to a stereoscopic supervision and data mining system and method facing lake blue-green algae disaster. The method comprises the steps that monitoring index data related to the lake blue-green algae disaster is obtained through the three ways of remote sensing monitoring, automatic monitoring and manual patrol inspect, and the obtained data is transmitted to a data center through the internet; the data center conducts data backup and data preprocessing on the received data, and temporal interpolation, spatial interpolation and abnormal decision processing are included; the data is transmitted to a database to be stored after being preprocessed; lake three-dimensional numerical model calculation is conducted according to a data source stored in the database, according to numerical model simulated data, to-be-monitored lake blue-green algae disaster risk evaluation is conducted, and lake blue-green algae disaster forecasting and early warning information is displayed on a public platform. According to the method and system, real-time stereoscopic monitoring on the blue-green algae disaster is achieved, collected data information is fully mined, data processing and model simulation are conducted, and blue-green algae disaster information real-time receiving, rapid and accurate processing and timely release are achieved.