The voltage or current harmonics and unbalancing have severe influence on control of various applications such as power quality devices, distributed generation systems, power converter devices, electric vehicle chargers and electric motors. Orthogonal d-q signals are significantly a part of controller for these applications. This paper proposes a new synchronization method based on integration average filter (AF) into conventional phase locked loop (PLL) in order to attenuate negative effect of voltage harmonics and unbalanced on orthogonal d-q signals for controller. Although some advanced techniques in the literature ensure good performances, uses of multiple filters reduce dynamic response and suffer from computational burden. The proposed improved AF-PLL has simple structure and implementation. It provides fast phase detection, fast dynamic response and removes ripple errors of voltage unbalance and harmonics. The performance of the filter-based PLL is evaluated in terms of balanced, unbalanced condition and harmonics distortion. The effectiveness and reliability of the proposed AF-PLL are demonstrated and discussed by means of comparative conventional PLL and advanced PLL in the literature. PSCAD/EMTDC is used for simulation and examination of all PLLs.