The 12-phase synchronous generator-rectifier system is widely used in mobile platforms that require high system security. In the system, the stator internal short circuit is a kind of common fault that may compromise the security of the generator. This paper gives detailed analysis on the internal phase-to-phase short-circuit faults, including the faults within the same group of Y-connected phases and those between different groups of Y-connected phases in the 12-phase system. A multiloop mathematical model is built to calculate all the voltages and currents when the faults occur in the system. In the model, the additional short-circuit loop between different phases, as well as the fault effects on both the air-gap magnetic field and the circuit topology of the system, are taken into account. Then a series of fault experiments are carried out on a 12-phase model machine. In view of the good agreement of experiment and simulation results, the effectiveness of the mathematical model and the simulation method is confirmed. Finally, the electric characteristics of the internal phase-to-phase short-circuit faults are summarized, and the fault mechanism is revealed.