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Alignment of the inertial navigation system (INS) in the mooring environment should take into account the movements of the waves or wind. The alignment of the INS is performed through an extended Kalman filter (EKF) using zero velocity as a measurement. However, in the mooring condition, this is not perfect stationary, thus the measurement error covariance matrix should be adjusted. In addition, if the measurement error covariance matrix is fixed to one value, the alignment time may take longer or the performance may be reduced depending on the change in mooring conditions. To solve this problem, we propose an alignment method using adaptive Kalman filter and convolution neural network (CNN)-based learning. The proposed method was verified for the superiority of alignment time and accuracy through Monte Carlo simulation in a mooring environment.