It is of great significance to study the brain structure and function in deep-tissue for neuroscience research and bio-medical applications because of the urgent demand for precise theranostics. Three-photon fluorescence microscopic (3PFM) bioimaging excited by the light in near-infrared IIb (NIR-IIb, 1,500-1,700 nm) spectral region is one of the most promising imaging techniques with the advantages of high spatial resolution, large imaging depth, and reduced scattering. Herein, a type of NIR-IIb light excitable deep-red emissive semiconducting polymer dots (P-dots) with bright 3PF and large three-photon absorption cross-section (σ₃) at 1,550 nm was prepared. Then the P-dots were functionalized with polystyrene polymer polystyrene graft ethylene oxide functionalized with carboxyl groups (PS-PEG-COOH) and modified with NH₂-poly(ethylene glycol) (PEG) to synthesis photochemically stable and biocompatible P-dots nanoparticles (NPs). Further the P-dots NPs were utilized for in vivo 3PFM bioimaging of cerebral vasculature with and without the brain skull under 1,550 nm femtosecond (fs) laser excitation. In vivo 3PFM bioimaging of the mice cerebral vasculature at various vertical depths was obtained. Moreover, a vivid three-dimensional structure of the mice vascular architecture beneath the skull was reconstructed. At the depth of 350 μm beneath the brain skull, 3.8 µm blood vessels could still be clearly recognized. NIR-IIb excitable P-dots assisted 3PFM bioimaging has great potential in accurate deep tissue bioimaging.