In this paper, we quantitatively characterize the morphological structure parameters including the nanopore size, shape, volume fraction, absolute number of nanopores and total prosity of polyacrylonitrile based carbon fiber precursor. Meanwhile, the change law and reason in the process of washing, drawing in washing, heat-densification, drawing in high pressure steam and hoting-stabilization are investigated. Results show that spinning drawing and high-temperature heat treatment make the prosity of fibers decline gradually in the process of fabrication. The result of micropore volume fraction Vi shows that at the beginning of the spinning and drawing in washing process the Vi of smaller nanopore which is less than 10 nm3 and the Vi of greater nanopore which is larger than 103 nm3 are 0.217 and 0.369, respectively, while these values sharply turn to 0.948 and 0.015 after the late spinning process of hoting-stabilization. The reason for this is not the increase of content of smaller nanopore content in the drawing process in high pressure steam and hoting-stabilization, but the sharp decrease of the greater nanopore content. The result about nanopore shape shows that the spinning multiple drawing in the process increases the axial (long-axis-to-short-axis) ratio of nanopores, while heat treatment over the glass transition temperature reduces the axial ratio of nanopore, and this shrinkage is more significant for smaller nanopores.