In this article, the novel adaptive neural networks (NNs) tracking control scheme is presented for nonlinear partial differential equation (PDE)-ordinary differential equation (ODE) coupled systems subject to deception attacks. Because of the special infinite-dimensional characteristics of PDE subsystem and the strong coupling of PDE-ODE systems, it is more difficult to achieve the tracking control for coupled systems than single ODE system under the circumstance of deception attacks, which result in the states and outputs of both PDE and ODE subsystems unavailable by injecting false information into sensors and actuators. For efficient design of the controllers to realize the tracking performance, a new coordinate transformation is developed under the backstepping method, and the PDE subsystem is transformed into a new form. In addition, the effect of the unknown control gains and the uncertain nonlinearities caused by attacks are alleviated by introducing the Nussbaum technology and NNs. The proposed tracking control scheme can guarantee that all signals in the coupled systems are bounded and the good tracking performance can be achieved, despite both sensors and actuators of the studied systems suffering from attacks. Finally, a simulation example is given to verify the effectiveness of the proposed control method.