Recent breakthroughs in molecular labeling and light microscopy enable the imaging of brain-wide neuronal population at cellular level. However, the development of neuronal reconstruction tools lags far behind massive datasets generation, which fails to meet the data analysis requirement at the current stage. In this sense, we first sought reasons for backwardness in current reconstruction tools and we summarized the features and introduced latest developments in these semi-automatic and fully automatic tools. Based on the summarized features, we further listed the challenges in developing reconstruction tools with high throughput and accuracy. In the end, we aired our views on the future development and application prospect of tools in neuron reconstruction.