In this study, polyamic acid salt-BNNTs (PAS-BNNTs) were prepared by noncovalently functionalizing water-soluble PAS with improved dispersion stability in organic solvents, and high compatibility with polyimide (PI) nanocomposites. We show that BNNTs functionalized with PAS have enhanced mechanical properties that are influenced by various loadings of PAS-BNNT/PI films through in situ polymerization. Compared with the pure PI film, the tensile strength and tensile modulus increased by about 20% and 37%, respectively. The proposed system also improved the coefficient of thermal expansion (CTE) from 52.6 to 45.7 ppm/oC. The enhanced mechanical properties of the PI nanocomposite were due to the interfacial bond strength enhanced by the reinforcing effect of PAS-BNNTs. Our study demonstrates the potential of PAS-BNNTs for preparing BNNT/PI nanocomposites with various structures.