Background: Substance use disorder is a chronic relapsing condition which requires longterm treatment. Client adherence is vital for effective methadone maintenance treatment (MMT). The objective of the present study was to identify effective factors and design an optimal management model for MMT clinics. Methods: A cross sectional, analytical and applied research was conducted involving 15 experts and 273 physicians.. In the qualitative section, the experts were interviewed using the purposive sampling method until the saturation of opinions. In the quantitative section, the physicians (experienced in addiction treatment) were included in the study. In the quantitative part, the instrument's reliability was evaluated by Cronbach's alpha index, and the validity of the instrument structure was evaluated by confirmatory factor analysis. Data were analyzed by SPSS sand Lisrel software. Results: According to the content validity confirmation, the reliability of the tool by Cronbach's alpha index shows values greater than 0.7, which indicates the reliability and repeatability of the tool. Also, the root mean square error of approximation (RMSEA) indices in all models show values less than 0.06 and chisquare index on the degree of freedom in all models less than 3, which shows the proper fit of the model and confirmation of the validity of the tool structure in the whole conceptual model. Conclusions: The effective factors in the management of MMT clinics include organizing, planning, controlling, guiding, leading, and managing treatment, which these dimensions can be an excellent basis for evaluating senior managers.