Background: A large number of natural disasters, including floods and earthquakes, occur in Iran annually. Recognition of the factors influencing the civil-military coordination in natural disasters is amongst the prerequisites in disaster management. Experts’ perspectives towards coordination in these disasters can also be indicative of the importance of this subject. Given the fact that no studies have been carried out regarding the relationship between the civil and military forces in the aftermath of natural disasters in Iran, these factors can be recognized according to individuals’ and experts’ viewpoints. Objectives: The present study aimed at extracting the factors influencing the civil-military coordination in the course of natural disasters in Iran through interviewing experts in 2019. Methods: The present qualitative research was conducted through semi-structured and in-depth interviews with 20 key informants who were selected via snowball, convenience, and purposive sampling methods. A session was also held with the presence of the panel of experts. The data were analyzed using thematic analysis in order to extract the factors influencing the civil-military coordination in natural disasters in Iran. Results: The factors influencing the coordination between the military and civil organizations were categorized into personnel, stuff, and system issues (structure). In addition, 33 subcategories were also identified. The specialists emphasized that holding instructional courses and regular and periodic exercises could enhance coordination in response to disasters. Conclusions: The present study showed that coordination between civil and military organizations in the management of natural disasters in Iran is faced with many challenges that should be overcome and reduced through providing organizational, political, and structural supports. Recognition of the factors influencing coordination can be effective in line with the correct management of natural disasters. Furthermore, organizations can be made readier for taking better measures in disasters according to the extracted factors. In order to provide a proper response to natural disasters, all coordination components should be elevated simultaneously and coherently.