The present application discloses a flexible excitation system and a method for controlling the same. The flexible excitation system consists of a plurality of groups of flexible excitation power units connected in parallel, a deexcitation circuit unit and a flexible excitation control unit. The method for controlling the flexible excitation system includes: realizing the internal fault-tolerant operation control of the flexible excitation power units by cooperatively controlling AC circuit breakers and DC circuit breakers of the flexible excitation power units and a deexcitation switch; dynamically controlling ceiling voltage when terminal voltage drops by using the fast response control ability of the flexible excitation system, so as to improve the forced excitation output capacity of the self-shunt excitation system. Aiming at the possible overload problem of an excitation transformer during the operation of flexible excitation, an excitation transformer overload limiter for the flexible excitation system is provided to limit the operation state of the excitation transformer within an allowable overload operation range of equipment.