Rapid development of the fifth-generation wireless communication technology (5G) has made electromagnetic interference (EMI) a critical threat to electronic operations and human health. To mitigate severe secondary scattering caused by impedance mismatch in traditional materials, this study proposes a chitosan-assisted self-assembly strategy for two-dimensional (2D) materials. Using directional freezing and freeze-drying, MXene@1T-MoS₂/chitosan composite aerogels with a lamellar porous structure were successfully fabricated. The regulatory effects of chitosan viscosity on microscopic morphology, conductive network construction, and shielding performance were systematically investigated. Results show that medium-viscosity chitosan induces an optimal layered skeleton, enabling sufficient multiple reflection losses within the aerogel. To further enhance absorption-dominated shielding, metallic 1T-MoS₂ was introduced to construct heterointerfaces. Characterization and electromagnetic analysis confirm that the synergy between 1T-MoS₂, MXene, and the chitosan matrix significantly enhances interfacial and dipole polarization losses. Experimental results indicate that the composite aerogels exhibit excellent EMI shielding performance in the X-band, with the absorption coefficient increasing by 0.14 after the introduction of 1T-MoS₂. Furthermore, far-field simulations reveal that the optimized aerogels achieve a remarkable radar cross-section (RCS) reduction, consistently maintaining scattered signal intensities below -20 dB·m² across a wide angular range. Mechanism analysis reveals that the high shielding efficiency stems from the organic synergy of conductive loss, multi-component-induced polarization loss, and multiple reflection effects triggered by the lamellar porous structure. This study successfully achieves a fundamental shift in the shielding mechanism from interfacial reflection to high-efficiency absorption, providing a new experimental basis and design strategy for developing lightweight, high-absorption EMI shielding materials.