Ag Se quantum dots (QDs) with near-infrared (NIR) fluorescence have been widely utilized in NIR fluorescence imaging in vivo because of their narrow bulk band gap and excellent biocompatibility. However, most of synthesis methods for Ag Se QDs are expensive and the reactants are toxic. Herein, a new protein-templated biomimetic synthesis approach is proposed for the preparation of Ag Se QDs by employing bovine serum albumin (BSA) as a template and dispersant. The BSA-templated Ag Se QDs (Ag Se@BSA QDs) showed NIR fluorescence with high fluorescence quantum yield (≈21.2 %), excellent biocompatibility and good dispersibility in different media. Moreover, the obtained Ag Se@BSA QDs exhibited remarkable photothermal conversion (≈27.8 %), which could be used in photothermal therapy. As a model application in biomedicine, the Ag Se@BSA QDs were used as "gatekeepers" to cap mesoporous silica nanoparticles (MSNs) by means of electrostatic interaction. By taking the advantages of NIR fluorescence and photothermal property of Ag Se@BSA QDs, the obtained MSN-DOX-Ag Se nanoparticles (MDA NPs) were employed as a nanoplatform for combined chemo-photothermal therapy. Compared with free DOX and MDA NPs without NIR laser, the laser-treated MDA NPs exhibited lower cell viability in vitro, implying that Ag Se@BSA QDs are highly promising photothermal agents and the MDA NPs are potential carriers for chemo-photothermal therapy.