Nanofibers from poly(lactic acid) (PLA) homopolymer and poly(p-dioxanone)-b-poly(ethylene glycol) multi-block copolymer (PPDO-b-PEG) with different phase separation morphologies depending on the crystallization induced self-assembly of PPDO-b-PEG are prepared by single spinneret electrospinning. Mixing solvents of chloroform-dimethyl formamide (CHCl3-DMF) with different compositions are used for controlling the crystallization of the PPDO block and therefore the phase separation in the obtained nanofibers. The crystallization of the PPDO block has a very important influence on the morphology of the PPDO-b-PEG nanoparticles in the spinning solution. In spinning solutions with low DMF content, nanoparticles with irregular shapes and non-compact inner structures are formed because the degree of crystallization of the PPDO block is relatively low, and a discontinuous sea-island phase separation is formed in the obtained electrospun nanofibers. Meanwhile, in spinning solutions with high DMF content, the copolymer can form flake-like nanoparticles with a relatively high degree of crystallization. The flake-like shape favors compact aggregation of the PPDO phase during formation of the nanofibers, and a continuous core-shell phase separation of the nanofibers is obtained.