This study introduces a novel deep modeling approach that utilizes Hamiltonian neural networks to address the challenges of modeling the six degrees of freedom rigid-body dynamics induced by control inputs in various domains such as aerospace, robotics, and automotive engineering. The proposed method is based on the principles of Hamiltonian dynamics and employs an inductive bias in the form of a constructed bias for both conservative and varying energies, effectively tackling the modeling issues arising from time-varying energy in controlled rigid-body dynamics. This constructed bias captures the information regarding the changes in the rigid body’s energy. The presented method not only achieves highly accurate modeling but also preserves the inherent bidirectional time-sliding inference in Hamiltonian-based modeling approaches. Experimental results demonstrate that our method outperforms existing techniques in the time-varying six degrees of freedom dynamic modeling of aircraft and missile guidance, enabling high-precision modeling and feedback correction. The findings of our research hold significant potential for the kinematic modeling of time-varying energy systems, parallel system state prediction and control, inverse motion inference, and autonomous decision-making in military applications.