This study aimed to investigate the relationship between administrative automation, organizational agility, and organizational health, considering organizational structure dimensions as a mediating variable in the General Department of Ports and Maritime Affairs of Bushehr Province. The current research is a descriptive-correlational study conducted cross-sectionally in the year 2025 among all employees of the General Department of Ports and Maritime Affairs of Bushehr Province. The total number of employees is 600, and from this number, 234 were selected as the sample size based on simple random sampling proportional to the population size and according to Cochran’s formula. To collect data, four questionnaires were used: Administrative Automation Questionnaire (Ahangarpour, 2008), Organizational Agility Questionnaire (Zhang & Sharifi, 2000), Organizational Health Questionnaire (Hoy & Feldman, 1996), and Organizational Structure Questionnaire (Robbins, 1979). The administrative automation questionnaire has 30 questions with validity and reliability of 0.90 and 0.93, respectively. The organizational agility questionnaire has 28 questions with validity and reliability of 0.88 and 0.86, respectively. The organizational health questionnaire has 44 questions with validity and reliability of 0.91 and 0.85, respectively. The organizational structure questionnaire has 24 questions with validity and reliability of 0.87 and 0.93, respectively. All statistical analyses were performed using SPSS and LISREL computer software. The results of data analysis indicate a significant relationship between administrative automation, organizational agility, and organizational health, considering the mediating variable of organizational structure dimensions in the General Department of Ports and Maritime Affairs of Bushehr Province. Conclusion: The organizational structure plays a very important role in achieving the organization’s goals, especially organizational health and agility, due to the type of service the organization provides.