Existing integrated refrigeration systems are decomposed into a refrigeration cycle and a process Heat Exchanger Network (HEN). To optimize the refrigeration cycle, the cycle is extended first to include all potential refrigeration options. Besides the complex refrigeration cycle, these options also generate a special HEN. A systematic method is proposed to optimize the complex cycle and the special HEN simultaneously. This method can give marginal prices of the refrigeration used as utilities in the process HEN. To improve the process HEN, the existing methods for HEN retrofit are used fully, based on the marginal prices of utilities from the refrigeration cycle. A strategy is proposed to co-ordinate the optimisation of the refrigeration cycle and the retrofit of the process HEN. Two case studies show how the proposed methods can retrofit the integrated refrigeration systems efficiently.