Scarce fault ride through capacity and unsteady output power are two vital problems in various in-grid doubly fed induction generators (DFIGs). This paper investigates an integrated DFIG protection scheme with a modified superconducting magnetic energy storage-fault current limiter (SMES-FCL). Based on proper parameter estimation of superconducting coil (SC) inside the SMES-FCL, modified controls of the SC and rotor side converter (RSC) are presented. Simulation results obtained from a 1.5 MW DFIG-based wind turbine case show that the proposed scheme is capable of limiting the peak values of fault rotor current, DC-link voltage and electromagnetic (EM) torque under symmetrical and asymmetrical faults, and thus to protect the RSC, gearbox and mechanical parts of the whole DFIG. With an additional positive-sequence d-q current modification control, this scheme is also discussed to lower the SC current capacity, to shorten the recovery time after grid faults, and to smooth the active power of the DFIG during normal operations.