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Energy loss reduction in power system is one of the most important issues in generation, transmission and distribution systems. The harmonic distortion which is generally injected by the non-linear loads to power system, is a significant factor increasing losses in power system. In order to eliminate these harmonics, active power filter is implemented. The appropriate generation of reference current is a main part of shunt active power filter control algorithm. In this article, the most common used theories for control and extraction of reference current in three-phase power system with non-linear load was simulated. Then the effect of selected method on active filter performance was analyzed and evaluated. A comprehensive comparison between control methods was performed in terms of harmonic cancellation and loss reduction capabilities, reactive power compensation, transient response speed and design requirement. The numerical results showed that “BPF” method has the best performance to improve total harmonic distortion (THD). In addition, voltage disturbances had no effect on its operation. However, this method did not represent good performance for unbalanced compensation. For this purpose, the using of reactive power theory (P-Q) was the most useful. The results showed that the selection of reference current generation method should be based on compensation purposes and design Limitations.