Separating raypaths in a multipath shallow-water environment is a challenge problem due to the interferences between them and colored noise existing in ocean environment, especially for two raypaths arrive close to each other. Thus, in this paper, a three dimensional (3D) higher-order raypath separation in an array to array configuration is proposed. Performance tests using simulation data in a multipath environment, real data obtained in an ultrasonic waveguide and ocean shallow-water data, respectively, illustrate that the proposed algorithm achieves a higher resolution and a stronger robustness comparing to the existing algorithms.