Dendritic spines are submicron scale protrusions on neuronal dendrites that form the postsynaptic sites of excitatory neuronal inputs. The morphological changes of dendritic spines reflect alterations in physiological conditions and are further indicators of various neuropsychiatric conditions. However, due to the highly dynamic and heterogeneous nature of spines, accurate measurement and object analysis of spine morphology is a major challenge in neuroscience research. Here, we propose an interactive 3D dendritic spine analysis system that displays 3D rendering of spines and plots the high-dimensional features extracted from the 3D mesh of spines in three graph types (parallel coordinate plot, radar plot, and 2D scatter plot with t-Distributed Stochastic Neighbor Embedding). With this system, analysts can effectively explore and analyze the dendritic spine in a 3D manner with high-dimensional features. For the system, we have constructed a set of morphological high-dimensional features from the 3D mesh of dendritic spines.