The 1064 nm NIR-II excitation of FD-1080 is demonstrated with the high tissue penetration depth and superior imaging resolution compared to NIR excitation from 650 nm to 980 nm. Deeptissue and high-resolution in vivo imaging for the left hindlimb vasculature, abdomen, and brain vessels were realized, allowing penetration through intact skin, tissue, and skull. It also quantifies the respiratory rate based on the dynamic imaging of respiratory craniocaudal motion of the liver for the awake and anaesthetized mouse.