Fluorescence probes emitting in the second near-infrared (NIR-II, 1000–1700 nm) window with the ability for deep-tissue imaging in mammals herald a new era in surgical methodology. However, the brightness of these NIR-II probes is still far from satisfactory due to their low fluorescence quantum yields (QYs), preventing the observation of high-resolution images such as whole-organ vascular networks in real time. Described here is the molecular engineering of a series of semiconducting polymer dots (Pdots) incorporated with aggregation-induced emission moieties to exhibit the QYs as high as 14% in the NIR-II window. Benefiting from the ultrahigh brightness, a 1400 nm long-pass filter is utilized to realize in vivo 3D tumor mapping in mice. To further understand how the geometrical and electron structures of the semiconducting polymers affect their optical properties, the in-depth and thorough density-functional theory calculations are performed to interpret the experimental results. This study lays the groundwork for further molecular design of highly bright NIR-II Pdots.