Large two-photon absorption cross section and high fluorescence quantum yield (QY) of a fluorescent probe is highly desirable to achieve high resolution in two-photon excited fluorescence imaging. Taking poly(9,9-dihexylfluorene-alt-2,1,3-benzothiadiazole) (PFBT) as an example, we report a one-step approach to synthesize PFBT loaded nanoparticles (NPs) with both large two-photon absorption cross section and high fluorescence QY in aqueous media through a micelle and silica coprotection strategy. The PFBT loaded NPs show a two-photon absorption cross section of 1085 GM at 810 nm based on polymer chain concentration and an emission maximum at 545 nm with a high fluorescence QY of 75%. The fluorescence lifetime investigation reveals that the high fluorescence QY is mainly due to reduced polymer aggregation and minimized environment influence on conjugated polymer (CP) fluorescence quenching. The synthesized PFBT NPs have shown good colloid stability and photostability as well as benign biocompatibility, which have been further applied to visualize the mouse brain vasculature through intravital two-photon excited brain vascular imaging with high contrast. The developed micelle/silica coprotection strategy should be generally applicable to other CP NPs with improved brightness and stability for various biological applications.