Abstract: Versatile molecular imprinting fluorescence sensors have been prepared for various species, but imprinting based fluorescent detection of target proteins upon different external stimuli is rarely reported. Herein, a novel phycocyanin-imprinted ratiometric fluorescence nanosensor was developed for temperature regulated sensing detection of target phycocyanin based on fluorescence resonance energy transfer (FRET). The nanosensor was fabricated by a simple facile copolymerization of amino/carboxyl modified quantum dots (QDs) as fluorescent supports, N-isopropylacrylamide as thermo-responsive functional monomer, N,N-methylenebis acrylamide as cross-linker and phycocyanin as template. Under the control of temperature at 20 °C and 45 °C, the fluorescence intensities of the QDs and phycocyanin were regularly decreased and enhanced at a different extent as the concentration of phycocyanin increased, respectively, and thereby the ratio of two fluorescence peak emission intensities of QDs and phycocyanin was used to determine the concentration of phycocyanin. Good linearity was obtained within 0-1.8 μM (r =0.9900) with a low detection limit of 3.2 nM, and excellent recognition selectivity towards the target phycocyanin was achieved over other proteins. Moreover, satisfactory recoveries of 92.0-106.8% were obtained in spiked seawater samples. The study provided a facile, fast and intelligent way for identification analysis of trace proteins from complex water matrices, and would push forward the protein imprinting and stimuli-responsive imprinting related researches