The in vivo spatio-temporal patterns of neovascularization are still poorly understood because it is limited to multi-scale techniques from the cellular level to living animal level. Owing to deep tissue-penetration and zero autofluorescence background, the second near-infrared (NIR-II, 1,000–1,700 nm) fluorescence imaging recently shows promise in breaking through this dilemma by dynamically tracking the pathophysiological process of neovascularization in vivo. Here, NIR-II fluorescence imaging was recruited for monitoring blood vessels in order to visualize the vascular injury and quantitively assess neovascularization in mouse models of acute skeleton muscle contusion and hindlimb ischemia. The temporal analysis of real-time NIR-II fluorescence intensity demonstrated that the blood flow perfusion of ischemia area was able to rapidly restore to 96% of pre-ischemic state within one week. Moreover, the spatial analysis revealed that the lower and outer quadrants of ischemia area in the mouse model of hindlimb ischemia always had relatively high blood flow perfusion compared with other quadrants during three weeks post-ischemia, and even exceeded pre-ischemic quantity at 21 days post-ischemia. In conclusion, this in vivo imaging technique has significant potential utility for studying the spatio-temporal patterns of neovascularization in vivo.