Nanostructure of ordered polyaniline-graphene (PANI-rGOPMAS) hybrid nanomaterials is assembled based on poly(2-methoxyaniline-5-sulfonic acid) (PMAS) functionalized reduced graphene oxide (rGOPMAS) nanosheets. The presence of PMAS not only improves dispersibility of reduced graphene oxide nanosheets, but also plays a key role for heterogeneous nucleation of polyaniline (PANI) nanorods. The formation mechanism of ordered PANI-rGOPMAS hybrid nanomaterials was studied in details by using field emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM) and ultraviolet-visible spectrophotometry (UV–vis). The conductivity of PANI-rGOPMAS hybrid with 17wt% rGOPMAS is as high as 4480S/m, compared with 2.93S/m for pure PANI. The cyclic voltammetry tests indicate that, PANI-rGOPMAS containing 2wt% rGOPMAS possesses fast response to redox reactions and excellent reversible stability. It has a high specific capacitance of 385Fg−1 at the scan rate of 10mVs−1 with potential ranges from −0.2 to 0.8V. This ordered polyaniline-graphene hybrid has potential applications for flexible supercapacitors, sensors, batteries, electromagnetic materials and thermoelectric materials, etc.