At present, the fabrication of three-dimensional (3-D) scaffolds possessing desirable nanotopography remains a significant challenge and an active research area. In this study, a highly porous, 3-D chitosan/poly(DL-lactic-co-glycolic acid) (PLGA) nanocomposite scaffolds featuring chitosan pores with interlaced PLGA nanofibers were produced by combining electrospinning and unidirectional freeze drying techniques. The porous structures of chitosan/PLGA nanocomposite scaffolds were characterized by scanning electron microscopy (SEM). In order to control the tubular morphology and nanotopography, different processing parameters, such as the concentration of chitosan solution and electrospinning time, have been extensively studied. The properties of chitosan/PLGA nanocomposite scaffolds, including the porosity, water absorption, modulus of compressibility, and compression strength, were also investigated. The results showed that a special 3-D tubular porous structure with PLGA nanofibers could be formed in the chitosan/PLGA nanocomposite scaffolds. The porosity and water absorption of the chitosan/PLGA nanocomposite scaffolds decreased with an increase in chitosan solution concentration and electrospinning time. In addition, the modulus of compressibility and the compressive strength of the chitosan/PLGA nanocomposite scaffolds increased due to the addition of PLGA nanofibers.