Materials possessing high two photon absorption (TPA) are highly desirable for a range of fields, such as three-dimensional data storage, TP microscopy (TPM) and photodynamic therapy (PDT). Specifically, for TPM, high TP excitation (TPE) brightness (σ × ϕ, where σ is TPA cross-sections and ϕ is fluorescence quantum yield), excellent photostability and minimal cytotoxicity are highly desirable. However, when TPA materials are transferred to aqueous media through molecule engineering or nanoparticle formulation, they usually suffer from the severely decrease of quantum yield (QY). Here, we report a convenient and efficient method for preparing polymer-encapsulated quantum dots (P-QD). Interestingly, the QY was considerably enhanced from original 0.33 (QDs in THF) to 0.84 (P-QD in water). This dramatic enhancement in QY is mainly from the efficiently blocking nonradiative decay pathway from the surface trap states, according to the fluorescence decay lifetimes analysis. The P-QD exhibits extremely high brightness (σ × ϕ up to 6.2 × 10(6) GM), high photostability, excellent colloidal stability and minimal cytotoxicity. High quality cellular TP imaging with high signal-to-background ratio (> 100) and tissue imaging with a penetration depth of 2200 μm have been achieved with P-QD as probe.