Uniform poly(lactic acid)/cellulose nanocrystal (PLA/CNC) fibrous mats composed of either random or aligned fibers reinforced with up to 20 wt % CNCs were successfully produced by two different electrospinning processes. Various concentrations of CNCs could be stably dispersed in PLA solution prior to fiber manufacture. The microstructure of produced fibrous mats, regardless of random or aligned orientation, was transformed from smooth to nanoporous surface by changing CNC loading levels. Aligning process through secondary stretching during high-speed collection can also affect the porous structure of fibers. With the same CNC loading, fibrous mats produced with aligned fibers had higher degree of crystallinity than that of fibers with random structure. The thermal properties and mechanical performances of PLA/CNC fibrous mats can be enhanced, showing better enhancement effect of aligned fibrous structure. This results from a synergistic effect of the increased crystallinity of fibers, the efficient stress transfer from PLA to CNCs, and the ordered arrangement of electrospun fibers in the mats. This research paves a way for developing an electrospinning system that can manufacture high-performance CNC-enhanced PLA fibrous nanocomposites.