Atmospheric duct is an anomalous structure with a high probability in the sea. Rough sea surface exists as an air-sea boundary, which can enable electromagnetic wave propagation more complex in atmospheric duct due to scattering. By the Fourier split-step algorithm of the standard parabolic equation and the impedance boundary conditions, the transmission loss in atmospheric duct for different kind of rough sea is analyzed. Numerical results show that the rough sea surface in atmospheric duct can increase significantly the loss of electromagnetic wave, and some blind area at the horizontal distance will disappear. But at the same time the electromagnetic energy loss caused by rough sea surface increases will also make the over-the-horizon detection more difficult.