The power extraction high voltage parallel reactor,referred to as energy extraction reactor, is essentially a hollow transformer consisting of grid-side windings and auxiliary windings. It belongs to a new type of reactor which can absorb the redundant reactive power of the system and provide the power supply for the station. At present, over-current or zero-sequence over-current protection is usually used in engineering to reflect the inter-turn short-circuit fault of the auxiliary windings. This protection scheme has some shortcomings, such as poor selectivity and long operation time. Therefore, in this paper, a new scheme of inter-turn winding short circuit protection for energy extraction reactor was proposed. The scheme integrates the voltage and current of the high reactance winding on the grid side and the current in the winding ring. It consists of the criterion of out-of-zone anomaly, the criterion of core saturation and the criterion of self-produced zero-sequence overcurrent in a logical phase. RTDS simulation results show that the protection scheme can not only ensure reliable operation under various non-regional fault conditions, but also reflect inter-turn short circuit fault of auxiliary winding more than 4%, and shorten the protection operation time to about 50 ms, thus solving the problems of poor selectivity and long operation time of previous inter-turn short circuit protection schemes for auxiliary winding.