This is the first study to systematically investigate the effectiveness of electrospinning parameters and solvent properties on the random and aligned poly (butylene adipate-co-terephthalate) (PBAT) fiber surface nanotopography. Therefore, the combinations of three groups of solvents, good solvents, and a non-solvent, were used. While THF (tetrahydrofuran), HFIP (1,1,1,3,3,3-hexafluoro-2-propanol) and DCM (dichloromethane) were selected as good solvents, DMSO (dimethylsulfoxide) was chosen as a non-solvent. Four different phase separation mechanisms, non-solvent-induced phase separation (NIPS), vapor-induced phase separation (VIPS), breath figure (BF), and thermally induced phase separation (TIPS) mechanisms, were applied to create roughness on the fiber surfaces. Smooth, porous and groove surfaces with average fiber diameters in the range of about 800–2000 nm were obtained at different electrospinning conditions by these phase separation mechanisms. Porous random fibers with a few small pores were obtained by NIPS in the presence of THF/DMSO, while corrugated random fibers were produced by VIPS with DCM/HFIP. The groove roughness on the aligned THF/DMSO and aligned DCM/HFIP fibers was achieved by the TIPS mechanism thanks to the rapid evaporation rate of THF and HFIP. The most porous fibers were obtained in the presence of moisture with a good solvent mixture of DCM/HFIP. The results of this investigation show that the use of good and non-solvents together with moisture control affected not only the topography of fibrous matrices but also the bulk characteristics of PBAT nanofibrous matrices.