The primary and secondary system configuration of a transformer air cooling control system is firstly introduced, and then aiming at the circumstance of multiple fan motors running in parallel in an air cooling control system, a new setting calculation scheme is proposed for multiple motors protection by using the total current of multiple motors. According to N-1 fault principle, setting values of each protection function are calculated in the new scheme based on the protection function configuration and its setting principle of a single motor relay. The sensitivity of all calculated setting values is analyzed in detail and the test is carried out by using a series of testing cases. The analysis and test result indicates that the new scheme has both high reliability and high sensitivity which can meet the demands of various protection functions for multiple motors in parallel operation, and also has certain practical value for motor protection in a transformer air cooling control system.