Mice are widely used in various physiological, pathological and behavioral experiments. However, it is yet unclear whether or how much spontaneous behavior varies between mice with different genotypes, which may affect experiment design and outcome. In this study, three inbred mice C57BL/6J, C57BL/6N, BALB/c (6J, 6N, BC) were selected, and objectively evaluated for their spontaneous behavior with a hierarchical unsupervised learning framework for 3D animal behavioral characteristics. The results showed that genotype is the most significant factors influencing mice, with the whole list presented as distant genotype＞near genotype＞gender difference. Behavior atlas varies greatly between BC and 6J/6N groups due to obvious differences in body posture, and BC have significantly lower movement speed than 6J and 6N. Although 6J and 6N behavior atlas were relatively similar, 6N sniffed significantly than 6J, and the anxiety levels at 6N were relatively high. The results of this study can be used as a reference for experiment design, strain selection, and determination of N value in future research using mouse model.