This invention disclosed is a comprehensive power quality controller for substation in the electric power system and includes a Thyristor Controlled Reactor (TCR), pure tuned passive filter Z.sub.f, additional inductor L active power filter (APF), and a coupling transformer. The Thyristor Controlled Reactor (TCR) provides inductive reactive power and controls the active power filter (APF) as the current source, it is connected with the additional inductor L.sub.a in parallel via the coupling transformer, then connected to the passive filter Z.sub.f in serial to consist a hybrid power filter system, which is connected to the power grid via the circuit breaker or thyristor. The comprehensive filter system provides required capacitive reactive power and filters the harmonic produced by the load and TCR system itself. Because the capacity of the active power filter (APF) is very small which is less than 1% of the harmonic source capacity, so it is a solution with low cost but simple and reliable control mode. It can suppress influence on the passive filter by the "background harmonic" of the substation and prevent the resonance occurred between the passive filter and power grid impedance.