<p>In economics, congestion occurs when an increase in some (all) inputs decreases some (all) outputs. Therefore, congestion is a kind of inefficiency because it causes the decision-making units (DMUs) to be inefficient and reduces their output. Identifying inefficient DMUs and determining the cause of their inefficiencies has been one of the most important reasons for referring to the internal scenario of DMUs and analyzing the effect of intermediate products on subDMUs (or stages) performance. The most important question that formed the basis of this research and we are looking for the answer: Is congestion rooted in the performance of intermediate products? This question is important because it seems that there is a hidden but inseparable relation between black-box (BB) congestion and two-stage processes. So, to characterize the congested DMUs and calculate their congestion, we looked at the internal structure of DMUs and analyzed the intermediate product’s effect and the subDMUs on the DMU's congestion. We can decompose the DMU's congestion into a BB and two-stage network congestion. We sought to state the relation between the BB input congestion and first stage input congestion. We have also identified subDMUs congestion and examined the relation between subDMUs congestion and the congestion of the DMUs as a whole. We define congestion in a two-stage network data envelopment analysis (DEA) conducted. We analyze and model the relation between subDMUs congestion and BB congestion to show the inputs of the DMUs involve two types of congestion (inputs as BB inputs and inputs as first stage inputs) while determining the relation between the two congestions. Finally, we have presented a practical example illustrating the proposed method.</p>