In this study, a novel flame-retardant and neutron-shielding additive was fabricated by the in-situ co-precipitation of gadolinium phenylphosphonate (GdPP) on boron nitride (BN) nanosheets. The resulting BN-GdPP heterostructures were incorporated with silicone rubber (SR) to produce a radiation protection composite. BN-GdPP/SR exhibited excellent mechanical properties, flame retardancy, smoke suppression, and thermal neutron shielding properties. The limiting oxygen index and UL-94 rating of BN-GdPP/SR were 34.19% and V-0, respectively. The peak heat release rate, total heat release, and total smoke production of BN-GdPP/SR decreased by 40.82%, 39.76%, and 32.60%, respectively, compared with those of pristine SR. The flame retardancy and smoke suppression were attributable to the synergistic effects between BN and GdPP. Moreover, owing to the homogeneous dispersion and horizontal orientation of BN-GdPP in the SR matrix, the tensile strength, thermal neutron shielding rate, and cross section of BN-GdPP/SR were 6.26 MPa, 89% (for 6 mm thickness), and 4.16 cm−1, respectively. This work provides a promising strategy for preparing high-performance multifunctional radiation shielding materials.