This study evaluates and analyzes the impacts of resilience engineering (RE) principles on integrated health, safety, environment, and ergonomics (HSEE) management system. In decision sciences, information should be reliable due to uncertainty and vagueness existing in information. To this end, in this study, the concept of Z‐numbers with fuzzy cognitive map (FCM) approach is integrated and a novel approach named Z‐number cognitive map is proposed. The main advantages of the proposed approach are determination of the weighted causality relations (for employing FCM) as well as handling uncertainty (for considering Z‐numbers concept). This approach is used to show the effects of RE indicators on HSEE management system. The required data for the proposed approach is collected from a large petrochemical plant by distributing questionnaires. According to the results, the RE principles have significant impact on HSEE management system. Top management commitment, learning, preparedness and awareness have the most impacts on environment, health, ergonomics and safety factors, respectively. This is the first study that employs Z‐number cognitive map for evaluating and improving the impacts of RE on HSEE factors in a large petrochemical plant. The proposed approach in this study, can help managers of various safety‐critical systems to improve their performance in terms of HSEE factors using RE concept.