The paper studies the intelligent decision support system, which is applied in intelligent warning system for colleges and universities public emergencies. Firstly, existing data of college emergencies is used to create decision support knowledge base. Then, the function model of the intelligent warning system is established, while the intelligence decision support algorithm of the intelligent warning system is proposed. At last, the intelligent warning system based on intelligence decision support is put forward, which can help avoid or mitigate it the occurrence of secondary derivative harm of the emergencies.