For conventional semiconductors, defect usually occurs on the surfaces to satisfy electron counting model, relax stress, and induce reconstructions. However, it is highly complex for BM-SrCoO2.5 (BM-SCO) and HSrCoO2.5 (HSCO) thin films because of oxygen vacancy channels (OVCs) in the bulk that can be considered as internal surfaces in addition to the most stable (001) surface. Therefore, it is unclear which surface provides the most preferred sites for H related defects to form. In addition, these defects may play significant roles in the phase transformation and magnetism tuning in the ionic liquid gating. To answer this question, we investigated the stability of the surfaces, H vacancies, and interstitials in HSCO using density functional theory. Unlike the general stability of H related defects in conventional semiconductors, the H vacancy prefers sites near the external surface or OVCs, while the H interstitial prefers sites of oxygen on a layer that contains six-fold coordinated Co in bulk because of the significant energy penalty by surface-induced local distortions and the crystal field splitting of Co atoms, exhibiting a weak ferromagnetism. These findings enrich the general understanding of complex surface phenomena of defect formation and provide an explanation of the good reversibility during phase transformation.