A comprehensive power quality controller combined with thyristor controlled reactor (TCR) and hybrid active power filter (HAPF) is described in this paper for substations in power system. The HAPF topology presented in the paper is different from the conventional HAPF. The basic of the new HAPF topology is to add a small inductor in parallel with the active power filter (APF) controlled as a current source, in order to force the fundamental current flow through the additional inductor instead of the APF. By this way, it can reduce the VA rating of the APF greatly. The TCR together with the passive filter part of the HAPF makes a static Var compensator (SVC), which acts as a classic reactive power compensator for load balancing and power factor correction. The small rating active filter is used to improve filtering characteristics of the passive filter in SVC and suppress possible resonance between the system impedance and the passive filter. The paper introduces the scheme's main circuit structure and its operation principle, mainly analyzes the control method and principle. Through modeling and simulation, the results verify the effectiveness and advantage of the comprehensive power quality controller for substations in power system.