The refining industry is under immense pressure to produce cleaner products but faces low economic margins because of stricter environmental regulations and depressed market demand. In this situation, refinery planning becomes very important as it can exploit all potential opportunities to push the economic margin to the maximum limit. This paper presents a method for overall refinery optimization through integration of the hydrogen network and the utility system with the material processing system. The problem of optimizing each of these three systems is very complex in its own right. To make the problem of overall optimization solvable, the current practice adopts a decomposition approach, in which material processing is optimized first using linear programming (LP) techniques to maximize the overall profit. Then, supporting systems, including the hydrogen network and the utility system, are optimized to reduce operating costs for the fixed process conditions determined from the LP optimization. Essentially these three systems are dealt with separately, which usually leads to nonoptimal solutions for refinery operations. A new optimization method is proposed that is developed on the basis of a sound understanding of interactions between the three systems and the proper use of mathematical modeling. This method considers the optimization of refinery liquid flows, hydrogen flows, and steam and power flows simultaneously. As a result, this method furnishes new insights into the problem of refinery optimization and can provide significant benefits to the refining industry in exploiting the true potential of the processes and obtaining truly optimal operation.