The dissociative culture technique of Aplysia neuron is one of the key methods that have been used for studies of cellular and molecular mechanisms of neuronal functioning. However, despite the advantages this method offers as an experimental model, its technical efficiency has had room for improvement. In this study, we examined certain putative factors that might affect the culture quality. The effects of neuronal damage induced by physical injuries, heat shock, and surface protein degradation were evaluated along with the correlation between the culture quality and animal behavior. As a result, we found that physical injury can be a critical factor that affects culture quality, whereas the heat shock and surface protein degradation had negligible effect on it. In addition, we discovered that siphon retraction time was not a good measurement for healthy neurons. Based on these findings, we suggest here an improved method in which the degree of physical injury is reduced by means of multiple protease treatment.