One of the important things to improve the efficiency of humanitarian aid logistics operations is to establish coordination between the various partners and stakeholders. This research has been conducted in this direction with the aim of identifying the factors affecting the coordination in the humanitarian supply chain and providing appropriate solutions. For this purpose, the techniques of Fuzzy Cognitive Mapping, Structural Equation Modeling, and Importance-Performance Analysis were used. A review of the literature and interviews with experts has led to the identification of 18 factors affecting coordination in the humanitarian supply chain, which were divided into five categories: strategic, infrastructure, cultural, process, and financial and non-financial resources. Factor analysis using Fuzzy Cognitive Mapping (FCM) showed that cultural cohesion and cooperation between partners was identified as the most important element. Also, the interpretive structural model of the main factors showed that the strategic, infrastructural and cultural factors were at the basic level. In addition, the importance-performance analysis was used in this study, which showed that in order to achieve better coordination in relief operations, long-term planning, providing efficient, effective and planned training, as well as mutual learning, should be considered. A potential practical implication is that actors involved in relief use the provided mechanisms such as operational and strategic planning and also the social implication is that by building trust and taking cultural considerations into account, it is possible to help better coordination of actors in crisis relief.