The refining industry is facing serious challenges because of severe market situations and stricter clean fuel regulations. To keep the competitive position, refineries have to implement nem processes or retrofit existing units, which require large amounts of capital. However, refineries are always short of capital because of low operating margins. Therefore, an efficient strategy for the debottlenecking refinery is highly desirable. In this paper, a new systematic approach is presented to deal with the debottlenecking issues in the overall refinery. In this two-stage approach, a mathematical model is proposed to identify processes that mostly constrain refinery profit. Then, the aim of the debottlenecking refinery is to shift bottlenecks from an expensive process to a cheaper process by modifying networks such as the hydrogen network and the utility system. In the second stage, other bottlenecks, which cannot be handled by the network changes, are retrofitted by using detailed process models to achieve the required extra capacity.