Every year, natural disasters in many countries lead to the destruction of infrastructure, loss of assets, and harm to the physical, mental, social, and spiritual health of people. The attention of policymakers and the media is mostly focused on the reconstruction of damaged buildings and the physical rehabilitation and recovery of the injured, while the spiritual rehabilitation of the people affected is often neglected. This study aims to identify the factors influencing the spiritual rehabilitation of people affected by natural disasters. This study was conducted using a systematic literature review following the PRISMA guidelines. Relevant studies were extracted from data sources, including MEDLINE (PubMed), Web of Science, Google Scholar, Embase, ProQuest, PsycInfo, Scopus, IranMedex, SID, and ISC. Systematic review studies, key journals, and conference proceedings related to the factors affecting the spiritual rehabilitation of individuals after natural disasters from January 1, 2020 to March 31, 2022 were included. Thematic analysis was used to analyze the obtained data. Initially, 1,753 studies were identified based on the initial search, and eventually, 22 final studies were included in the study. Based on the thematic analysis results, the factors influencing the spiritual rehabilitation of people affected by natural disasters were classified into four main themes and eleven sub-themes. The main themes included communication with God, strengthening religious beliefs, social participation, and meaning-making. The sub-themes included praying, using supplication, reading the holy book, praising God, believing in the afterlife, understanding the position and characteristics of the world, understanding the divine, participating in religious ceremonies, membership in supportive groups, the meaning of suffering and adversity, and the meaning of death. The results of this study demonstrate that the connection with the divine (God), strengthening religious beliefs, social participation, and meaning-making are influential factors in the spiritual rehabilitation of affected people after natural disasters. Incorporating these factors in the spiritual counseling and care of the affected people can improve their spiritual health after encountering the destructive effects of natural disasters. These findings can provide valuable insights for managing natural disasters through a holistic approach to the health of affected people, and can guide caregivers in implementing spiritual rehabilitation interventions.