Four new diamines (3TFDABA, 2TFDABA, 22TFDABA and TFAPTA) were successfully synthesized to investigate the effect of different trifluoromethyl (CF3) substitution position on poly(amide-imide)s (PAIs) properties. High-performance PAIs were prepared from high-temperature polycondensation of these diamines with 6FDA dianhydride. All the PAI films exhibited good heat resistance with glass-transition temperatures (Tgs) of 311–392 °C, good 5% weight loss temperatures (Td5%s) of 480–510 °C in nitrogen, and excellent optical transparency with T450 ranging from 52% to 84%. According to the monomer structural design, a high heat resistant and colorless poly(amide-imide) film (PAI-2-6FDA), with excellent optical properties (T450 of 82%), outstanding thermal properties (Td5% of 499 °C and Tg of 392 °C), and good mechanical properties (tensile strength of 123 MPa, tensile modulus of 4.4 GPa) was achieved. A comprehensive structure-to-property relationship study revealed that the CF3 in ortho-position of the amino group effectively inhibited the rotation between imide ring and benzene, thus improved the heat resistance of the film. Moreover, it could also weaken the generation of charge transfer complexes through strong electron-withdrawing ability, which is beneficial for the synthesis of colorless polyimides.