For the design of large hydro-generator with perfect paralleled-branches number and rated speed, the asymmetric windings are more widely adopted nowadays. Due to the special connection of the armature winding, the fault characteristics of the internal short-circuits in the asymmetric winding are different from those of the conventional symmetrical winding. Taking a 4-branches asymmetric winding generator as the research object, the characteristics of all the possible internal faults are analyzed in detail, and the fault currents distribution is calculated with the multi-loop method. Then the optimized protection configuration is obtained in the nonadjacent branch-grouping mode of the generator, composed of the split-phase transverse differential protection, complete longitudinal differential protection and zero-sequence current transverse differential protection. Comparing with another scheme shows that, the operation rate and the double-protection rate of the optimized scheme meet a high technical standard.