In this paper, a novel wide area measurement system (WAMS) based distance protection scheme for parallel transmission lines is proposed. This protection scheme sufficiently utilizes the information in WAMS to set up an accurate system model in remote terminal. Then the proposed scheme uncouples the model into a six-sequence mathematical model to eliminate the influence of the zero-sequence mutual inductance. Along with the uncoupled model, a linear equation in frequency domain, without any theoretical error, is given and the fault distance and fault resistance can be obtained by solving the equation with fundamental frequency component and aperiodic component. To verify the proposed algorithm, many simulations based on PSCAD are performed in this paper. Simulation results show that the proposed scheme eliminates the influence of the zero-sequence mutual inductance. It can calculate the fault distance accurately and have high tolerance to fault resistance.