The cooperative system, such as cyber-physical systems (CPSs) and system of systems (SoSs), are systems that operate with collaborations between numerous heterogeneous systems to accomplish common goals of the systems. These systems are often safety-critical systems since they are increasingly used to perform safety-related activities. Therefore, it is one of the important behavior to assure the safety of such systems by identifying potential hazards that lead to the accident by appropriate hazard analysis techniques. Due to the nature of the cooperative systems, such as dynamic changing structures or existing unknown number of configurations during operations, it is necessary to consider such possible dynamic structures in the hazard analysis. However, there are several limitations to identifying hazards associated with such uncertainties through the existing hazard analysis approaches. This paper proposes an approach of hazard analysis considering dynamic configurations for cooperative or collaborative systems. The proposed approach constructs a variability information model from several system specifications and traceability analysis results and provides approach of using such information to the hazard analysis. We also performed a case study to show the feasibility of the proposed approach with the vehicle platooning system, which is a kind of cooperative automotive system.