Maritime safety issues have aroused great attention, and it has become a difficult problem to use the sky-wave over-the-horizon radar system to locate foreign targets or perform emergency rescue quickly and timely. In this paper, a distributed multi-point sky-wave over-the-horizon radar system is used to locate marine targets. A positioning algorithm based on the Doppler frequency is proposed, namely, the two-step weighted least squares (2WLS) method. This algorithm first converts the WGS-48 geodetic coordinates of the transceiver station to spatial rectangular coordinates; then, introduces intermediate variables to convert the nonlinear optimization problem into a linear problem. In the 2WLS method, four mobile transmitters and four mobile receivers are set up, and the Doppler frequency is calculated by transmitting and receiving signals at regular intervals; it is proven that the 2WLS algorithm has always maintained a better positioning accuracy than the WLS algorithm as the error continues to increase with a certain ionospheric height measurement error and the Doppler frequency measurement error. This paper provides an effective method for the sky-wave over-the-horizon radar to locate maritime targets.