Lightweight, flexible, heat-resistant neutron shields are required for nuclear and aerospace applications. Conventional polymer composites face a trade-off between high filler loading and flexibility, along with limited thermal stability. Herein, we present an aqueous in-situ polymerization strategy to fabricate boron nitride nanotube (BNNT)–dispersed polyimide (PI) films at high BNNT content. A water-borne poly(amic acid) salt (W-PAAS) enables one-pot processing, maintaining homogeneous BNNT dispersion and suppressing re-aggregation during film formation. Notable neutron attenuation was achieved using stacked films composed of sub-100 μm individual layers, reaching μ = 1.67 mm⁻¹ and μ/ρ = 9.23 cm² g⁻¹ for PIBT-60. This performance is attributed to moderation by the hydrogen-rich PI matrix and absorption by uniformly dispersed BNNTs. Even at high BNNT loading, films remain flexible (R = 2.5 mm) and thermally stable (T_d,5% > 600 °C).