The formation of dorsal-ventral axis of the spinal cord is controlled largely by dorsal signals such as Wnts (which are members of the wingless + MMTV integrants, Int family), besides ventral signals such as sonic hedgehog (Shh). Wnt3a, one of the Wnt family members, is involved in multiple cellular functions, including self-renewal, proliferation, differentiation, and motility. Here, we aim to study the mechanism of the regulation of chicken spinal cord patterning by Wnt3a. In this study, Wnt3a was ectopically expressed in the spinal cord of developing chicken embryos by in ovo electroporation. The results of immunofluorescent staining revealed that Wnt3a ectopic expression caused the abnormality of commissural axonal projection and the formation of nerve fibers was interrupted. It is worth noting that neurons in the ventricular zone, especially motor neurons, could not migrate laterally after the Wnt3a overexpression, which led to the malformation of motor column. In addition, we found that neurons could not protrude axons outwardly after overexpression of Wnt3a in the spinal cord. It was also found that Wnt3a overexpression inhibited the outgrowth of processes in culturing SH-SY5Y cells. In conclusion, we proposed that Wnt3a regulates neuronal morphology, which subsequently disrupts axonal projection and motor neuron positioning during spinal cord development.