Conventional polyimide nanocomposites reinforced with graphene-based nanofillers usually possess excellent properties, such as high thermal decomposition temperature, enhanced tensile strength, tensile modulus, etc. However, the elongation at break of the nanocomposites is reduced. Here,we prepared N-doped graphene quantum dots/colorless polyimide nanocomposite (N-GQDs/CPI) films for the first time by in-situ polymerization, whose elongation at break is about 2 times that of the pure film. Meanwhile, the thermal properties and other mechanical properties of the films are improved. Through analyzing FT-IR, XPS, XRD, TAG SEM, etc. of N-GQDs and the films, we consider that the strengthening mechanism of matrix performance is attributed to N-GQDs' well dispersion, its small size effects and strong interface interaction with the matrix. Furthermore, at the indicativewavelength of 550 nm, the optical transmittance of the filmwith 1wt% N-GQDs stillmaintains 79%, indicating the resulting films have excellent optical transmittance. The hydrophilic properties of the prepared films' surface is reduced, their water surface contact angle are increased from 63 ± 2.7° to 92 ± 1.7° with the content of N-GQDs increasing. This research shows that N-GQDs can enhance the various properties of polyimide and provides a high performance nanocomposite films for potential flexible substrates.