Objective To assess the results of Fluoro Jade-c (FJC) staining in brain injury after deep hypothermia circulatory arrest (DHCA). Methods First, animal model of DHCA were established. We performed DHCA on six Chinese experimental minipigs and made sure all the pigs were alive after operation. Second, pathological examination was carried out on the brain tissues of these animals. After FJC staining, we respectively took out the positive and negative tissueparts and performed Hematoxylineosin (HE) staining, Nissl staining and Terminal deoxynucleotidyl Transferase BiotindUTP Nick End Labeling (TUNEL). Finally, the results of FJC was compared with TUNEL, Nissl staining, HE staining, to verify the accuracy and reliability of FJC in assessing brain injury after DHCA. Results Postoperative FJC staining discovered positive disease focuses on the experimental pigs. The comparative results of FJC were consistent with TUNEL (Kappa=0.526, Plt;0.01), Nissl staining (Kappa=0.555, Plt;0.01) and HE staining (Kappa=0.491, Plt;0.01). However, FJC staining image was much clearer and easier in identifying brain injury. Conclusion FJC is a reliable and convenient method to assess brain injury after DHCA.