Morphological retrieval is an effective approach to explore neurons' databases, as the morphology is correlated with neuronal types, regions, functions, etc. In this paper, we focus on the neuron identification and analysis via morphological retrieval. In our proposed framework, both global and local features are extracted to represent 3D neuron data. Then, compacted binary codes are generated from original features for efficient similarity search. As neuron cells usually have tree-topology structure, it is hard to distinguish different types of neuron simply via traditional binary coding or hashing methods based on Euclidean distance metric and/or linear hyperplanes. Thus, we propose a novel binary coding method based on the maximum inner product search (MIPS), which is not only more easier to learn the binary coding function, but also preserves the non-linear characteristics of neuron morphology data. We evaluate the proposed method on more than 17,000 neurons, by validating the retrieved neurons with associated cell types and brain regions. Experimental results show the superiority of our approach in neuron morphological retrieval compared with other state-of-the-art methods. Moreover, we demonstrate its potential use case in the identification and analysis of neuron characteristics.