This study took four coastal counties in Ningde as examples to carry out risk assessment of harmful algal blooms (HABs) disaster. The index systems of risk assessment of HABs disaster were established based on leading, measurable and available principles. The weights of evaluation indexes were determined by entropy method. In addition, hazard assessment model, vulnerability assessment of hazard-bearing body model and risk assessment model were set up, respectively. Finally, this study utilized GIS platform to realize visualization of the assessment results. The research revealed that the HABs with the medium risk were detected along Fuding coast and Xiapu coast. Along Jiaocheng coast and Fuan coast, HABs caused low risk. The evaluation results are consistent with the historical data, actual situation and related literature of HABs in the east coast of Fujian. This paper provides technical support for HABs monitoring, disaster prevention and mitigation and aquaculture.