Customs have an important role in the supply chain. With increasing in traded goods and diversification of the international trade, controls of traditional customs cannot create value for the business community. Implementation of Post-Clearance Audit (PCA) is a part of the customs' modernization strategy. Introducing PCA reflects a different approach to customs' control, as it has the effect of offering an immediate release of goods or reduced release time. This study attempts to provide a national roadmap by modeling of PCA and its utilization effects in the Islamic Republic of Iran Customs have been considered. We used Structural Equation Modeling (SEM) to construct a conceptual model and used AMOS software to estimate model parameters and assessment of its validation, too. We tested goodness of model fit by Chi-square index. The results indicated that the conceptual model was valid and according to the model, PCA should be performed on a national auditing standards foundation. By application of a PCA, standards-based approach, Customs would be able to target their resources more effectively and work in partnership with the business community to improve compliance levels and facilitate trade. Thus, capacity building of human resource, identification of Authorized Economic Operator (AEO) and their relevant indexes, are our suggestions.