Robust and accurate pose estimation with multi-modal sensors is fundamental for autonomous vehicles and mobile robotic systems in complex environments. In this paper, we propose DAP-Pose, a unified end-to-end model for robust multi-modal pose estimation. DAP-Pose introduces a Bi-level Cross-modal Fusion (BCF) module that captures complementary semantic and geometric motion cues from visual, inertial, and GNSS measurements. To handle temporal offsets, we designed a Deep Temporal Alignment (DTA) module that explicitly aligns asynchronous streams in latent space, enabling coherent motion modeling without strict hardware synchronization. Furthermore, we incorporate physics-aware constraints via manifold geometry and GNSS-guided absolute metric scale, enforcing motion consistency and mitigating drift. Experiments upon the public KITTI benchmark dataset were conducted to evaluate the performance of DAP-Pose against existing methods. DAP-Pose achieved the state-of-the-art performance, with the lowest average translation error ($t_{rel}$) of 1.31% and rotation error ($r_{rel}$) of 0.46$^{\circ}$. Furthermore, it accurately estimates poses and maintains robust performance under severe artificially injected temporal misalignment.

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