This paper presents the comparison of specific exergy costing (SPECO) and modified productive structure analysis (MOPSA) method to test their abilities on costing of exergy destruction. MOPSA method is applied to a combined supercritical CO(2)regenerative cycle and organic Rankine cycle using zeotropic mixtures for gas turbine waste heat recovery system. The results obtained with applying SPECO method to the system are taken from literature. The exergy destruction cost rate of overall system is obtained to be $86.08/h and $1,113.13/h for MOPSA and SPECO methods, respectively. The exergoeconomic factor of overall system is found to be 31.88% for SPECO method, while this value is found to be 85.82% for MOPSA method. The obtained results with applying MOPSA method for exergy destruction cost rate are significantly lower and more consistent compared to the results obtained by SPECO method.