This study provides a new embedded linear model (ELM) three-dimensional fuzzy PID control method for a bionic autonomous underwater vehicle (AUV), which is disturbed by ocean waves. The uncertainty of the ocean waves will make it difficult for the AUV to achieve good sailing quality, especially near the sea surface. In view of this problem, an ELM fuzzy PID controller, which adopts three-dimensional fuzzy control rules, is designed. In the ELM fuzzy PID controller, a linear model of AUV is established in order to actively perceive the effect of waves on AUV. Hence, the wave disturbance can be reflected in the control signal earlier and faster. Finally, three simulations are carried out to verify the control effect of the ELM fuzzy PID controller. An ocean wave disturbance model is established in order to simulate the force and the moment acting on the AUV. The results imply that compared with the classical PID controller and normal fuzzy PID controller, the ELM fuzzy PID controller can significantly enhance the stability of AUV and make the response faster and overshoot smaller.