Herein, we have developed a rather simple composite fabrication approach to achieving molecular-level dispersion and planar orientation of chemically modified graphene (CMG) in the thermosetting polyimide (PI) matrix as well as realizing strong adhesion at the interfacial regions between reinforcing filler and matrix. The covalent adhesion of CMG to PI matrix and oriented distribution of CMG were carefully confirmed and analyzed by detailed investigations. Combination of covalent bonding and oriented distribution could enlarge the effectiveness of CMG in the matrix. Efficient stress transfer was found at the CMG/PI interfaces. Significant improvements in the mechanical performances, thermal stability, electrical conductivity, and hydrophobic behavior were achieved by addition of only a small amount of CMG. Furthermore, it is noteworthy that the hydrophilic-to-hydrophobic transition and the electrical percolation were observed at only 0.2 wt % CMG in this composite system. This facile methodology is believed to afford broad application potential in graphene-based polymer nanocomposites, especially other types of high-performance thermosetting systems.