Structure of nano amorphous matter has not been studied sufficiently yet due to the difficulty in both operation of nano matter and characterization of their structure. In this work, a detailed study of the structural orientation within amorphous polymeric nanofiber and its mechanical strength was conducted for a highly thermal resistant amorphous polymer: poly(phthalazinone ether ketone) (PPEK). Poly(butylene terephthalate) (PBT), a semi-crystalline polymer with partial difference in chain flexibility and geometry to PPEK, was chosen for a comparative discussion. For the method, highly aligned PPEK and PBT nanofiber bundles were prepared by electrospinning with a home-made book-like collecting device. X-ray experiments were conducted to research their structural orientation, and tension experiments were conducted to research their mechanical properties. It was found that the amorphous PPEK nanofibers showed relatively low orientation degree of polymer chain limited by its rigid and twisted segments within the polymer chain, while PBT nanofibers showed not only highly ordered crystal structure but also very large shish length, beneficial from the co-existence of rigid and flexible segments. The above structural information was well supported by their uniaxial tensile behaviors, where PBT nanofiber manifested much larger ultimate stress sigma, failure strain epsilon, Young's modulus E and toughness than those of PPEK nanofibers and commercial PBT plastic. However, the electrospun PBT nanofibers' orientation degree, within the range of 0.45-0.7, is much lower than that of some reported melt-spun PBT fibers with the orientation degree above 0.9. Therefore, it can be concluded that the instinct characterization of polymer chain and processing technique have a much more significant influence than size effect on the structural orientation and mechanical strength of nanofibers rather than size effect.