In this paper, an orthogonal crossover artificial bee colony (OCABC) algorithm based on orthogonal experimental design is presented and applied to infer the marine atmospheric duct using the refractivity from clutter technique, and the radar sea clutter power is simulated by the commonly used parabolic equation method. In order to test the accuracy of the OCABC algorithm, the measured data and the simulated clutter power with different noise levels are, respectively, utilized to estimate the evaporation duct and surface duct. The estimation results obtained by the proposed algorithm are also compared with those of the comprehensive learning particle swarm optimizer and the artificial bee colony algorithm combined with opposition-based learning and global best search equation. The comparison results demonstrate that the performance of proposed algorithm is better than those of the compared algorithms for the marine atmospheric duct estimation.