Polyimide (PI) is one of the most dominant engineering plastics with excellent thermal, mechanical, chemical stability and dielectric performance. Further improving the versatility of PIs is of great significance, broadening their application prospects. Thus, integrating functional nanofillers can finely tune the individual characteristic to a certain extent as required by the function. Integrating the two complementary benefits, PI-based composites strongly expand applications, such as aerospace, microelectronic devices, separation membranes, catalysis, and sensors. Here, from the perspective of system science, the recent studies of PI-based composites for molecular design, manufacturing process, combination methods, and the relevant applications are reviewed, more relevantly on the mechanism underlying the phenomena. Additionally, a systematic summary of the current challenges and further directions for PI nanocomposites is presented. Hence, the review will pave the way for future studies.