The invention discloses a transformer substation acceptance inspection working process control system and control method with the function of intelligent warning and prompting. The system is composed of an intelligent warning device, a rule determination module, a process transferring module, a main controller, a timing device, a storage device, a data processing module, and an automatic checking module. The acceptance inspection work of the transformer substation includes: substation acceptance inspection application, inputting of point table information and a protection configuration table, information table preprocessing and examination and approving of acceptance inspection application, master station pattern drawing and system configuration of the master station and substation, inputting of a monitoring information table, substation acceptance inspection, master station acceptance inspection, examination and acceptance reporting, casual inspection of acceptance inspection results, and formation of final acceptance reports and evaluation reports. According to the invention, information missing during the acceptance inspection process can be avoided; coordination of work of all departments can be realized and errors caused by handing over of departments can be avoided; the work efficiency can be improved; high accuracy and high efficiency of the acceptance inspection work of the transformer substation can be guaranteed; the accuracy of the power equipment acceptance can be improved based on the standard acceptance inspection mode; and secure and stable operation of the power grid can be guaranteed.