Stray currents from DC metro systems intrude into the grounded neutrals of large power transformers, posing a major threat to the differential relay protection of transformer. In this paper, the performance of harmonic blocking based differential relay protection considering neutral stray currents (NSCs) from DC metro systems is thoroughly investigated. The findings reveal that relays may fail to clear internal faults in some scenarios because they are blocked due to NSC-induced harmonic currents. To improve the reliability of differential relay protection, a method for preventing incorrect operation is proposed using a skewness-based criterion to detect the presence of NSCs. Then, the relay is unblocked when an internal fault is simultaneously detected by the novel internal fault detection block. The proposed method is resistant to current transformer saturation and accounts for NSC fluctuations. Various time-domain simulations conducted in PSCAD/EMTDC verify the effectiveness of the proposed method.