The invention relates to an intelligent warning system based on integer programming. The intelligent warning system adopts a signal acquisition module, a diagnostic startup judgment module, a fault analysis module, a failure report generating module and an analytical result comprehensive display module to warn; the intelligent warning system can be implemented through the following steps of: 1) network modelling, filling primary equipment of a transformer substation and a connected relation of the transformer substation into a database; and generating a structural model meeting IEC (international electrotechnical commission) 61970 standard of an electric system factory station and a system, and then using the model to generate a network device library through a filling library operation; 2) protected information modeling: carrying out protected information modeling according to the hierarchical relationship of the primary equipment, a protective device, protected information and a trip breaker, building an incidence relation between a protection main device, the protected information and a breaker motion, and protecting the main device namely the primary equipment; and 3) carrying out fault diagnosis. The intelligent warning system in the invention can be capable of rapidly and effectively carrying out detailed analysis on a single or complicated failure and protection motion analysis in a failure process.